runCrossSample tool

[pcm32]

@emily101-gif I have fixed the galaxy issues of the tool, but the tests are currently not passing because the flowstat3 test files are not equivalent to what the tool is outputting. Currently output1.flowstat3 and output2.flowstat3 files have around 16 more lines than the outputs generated by the tools:

JobOutputsError: History item  different than expected, difference (using diff):
( /var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmp8VmHXbout1.flowstat3 v. /var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmpO7Fkyxout1.flowstat3 )
--- local_file
+++ history_data
@@ -1,27 +1,27 @@
 Population FSC_mean    FSC_median  FSC_stdev   SSC_mean    SSC_median  SSC_stdev   CD4_mean    CD4_median  CD4_stdev   CCR7_mean   CCR7_median CCR7_stdev  CD8_mean    CD8_median  CD8_stdev   CCR3_mean   CCR3_median CCR3_stdev  Percentage_mean Percentage_median   Percentage_stdev
-1  362.36  362.36  2.03    115.66  115.66  4.69    520.22  520.22  2.1 187.01  187.01  8.0 49.3    49.3    1.43    71.62   71.62   6.22    9.53    9.53    0.92
-2  434.28  374.35  111.03  173.06  125.62  92.77   481.01  521.93  74.19   53.87   39.72   27.49   123.6   72.0    94.92   262.34  197.55  140.75  4.77    5.35    4.11
-3  387.79  395.7   23.62   130.91  119.3   27.93   435.9   410.23  67.59   74.72   69.3    9.68    600.1   585.6   29.27   329.66  275.2   135.27  3.65    0.15    6.14
-4  362.46  363.32  6.82    204.27  204.11  37.15   89.98   96.34   14.26   176.99  147.5   52.47   99.4    102.85  11.5    379.43  318.19  129.33  2.15    0.42    3.06
-5  325.38  320.36  10.17   160.67  155.29  19.56   59.04   56.73   12.13   89.3    81.95   21.59   86.04   73.35   29.85   138.09  112.25  52.08   3.85    4.61    3.27
-6  368.28  368.59  11.22   150.66  148.89  19.84   72.55   69.32   5.76    104.15  96.05   37.15   610.48  612.42  3.86    266.97  244.06  45.55   6.11    3.08    6.26
-7  396.63  403.26  20.5    168.46  176.59  16.14   87.66   94.51   12.08   279.23  281.53  86.3    621.35  620.71  1.55    304.29  274.19  61.37   3.9 2.99    1.61
-8  404.55  404.55  47.31   144.35  144.35  45.71   517.41  517.41  0.11    341.18  341.18  115.72  460.13  460.13  258.52  471.42  471.42  48.2    5.63    5.63    7.93
-9  411.14  431.34  58.13   304.59  331.2   81.01   255.21  292.9   108.35  576.55  562.5   181.39  376.48  302.14  136.76  558.62  616.89  126.67  0.5 0.18    0.68
-10 355.5   355.5   4.74    112.88  112.88  3.84    520.08  520.08  0.38    31.22   31.22   1.9 58.0    58.0    5.33    67.4    67.4    6.98    8.64    8.64    1.69
-11 388.08  388.08  10.53   168.48  168.48  47.07   104.65  104.65  27.37   274.21  274.21  231.97  638.98  638.98  51.13   538.17  538.17  51.43   4.54    4.54    6.28
-12 428.71  421.38  16.73   335.25  241.15  165.09  130.58  120.19  22.63   198.19  205.92  43.13   212.07  215.97  22.59   168.98  147.47  50.14   2.43    3.0 1.21
-13 421.73  423.08  14.71   183.94  195.44  42.68   437.73  405.31  69.88   414.28  421.76  139.69  610.61  615.38  23.29   289.5   289.23  16.72   3.73    0.19    6.24
-14 373.78  363.33  22.49   142.58  136.41  43.0    448.64  460.06  83.19   598.24  567.5   67.94   234.64  77.56   279.04  158.48  164.12  43.29   1.61    0.08    2.68
-15 369.71  361.32  20.31   147.49  118.97  54.51   306.98  301.48  35.15   122.87  109.52  49.72   115.48  71.4    78.14   148.68  117.17  67.47   1.09    1.42    0.74
-16 419.18  419.08  14.47   284.65  264.01  99.6    107.66  107.35  12.52   479.28  510.36  61.47   134.26  130.48  13.97   198.02  201.21  28.44   1.41    0.58    1.51
-17 472.22  462.0   27.16   267.49  196.73  134.04  485.32  512.67  55.91   591.9   588.96  124.73  284.97  357.2   145.9   346.39  284.33  116.55  0.55    0.12    0.84
-18 391.3   388.6   9.62    151.22  132.42  42.06   468.62  525.67  101.55  200.8   197.56  12.67   150.61  64.27   151.76  251.49  205.87  109.27  4.37    5.28    3.77
-19 954.49  948.66  16.08   990.53  979.64  20.85   494.76  496.89  16.58   627.61  649.92  62.61   526.51  498.02  54.65   525.11  507.34  59.97   0.55    0.48    0.14
-20 420.28  431.49  23.44   220.23  175.21  96.79   128.13  108.33  59.81   528.18  547.09  71.02   636.01  620.52  55.87   359.88  338.83  106.83  2.7 0.53    4.19
-21 611.37  612.66  8.09    969.24  967.97  7.2 141.84  140.47  2.77    223.33  220.24  7.11    223.8   216.74  15.51   183.19  176.15  32.07   14.7    14.78   1.9
-22 666.05  677.97  29.25   452.57  434.17  32.95   377.8   376.69  16.57   226.24  215.63  23.58   212.9   192.78  35.36   277.65  267.15  39.06   2.22    2.36    0.64
-23 546.68  550.94  8.1 989.48  988.58  2.38    361.98  358.59  13.74   472.15  469.96  9.68    381.26  366.78  27.25   438.45  411.62  57.08   1.72    1.77    0.32
-24 683.11  692.69  31.65   446.21  473.52  51.33   394.62  397.71  7.78    202.01  214.78  26.42   192.77  183.47  31.32   148.62  143.66  27.39   2.14    2.2 0.53
-25 727.79  726.15  4.62    1017.52 1017.01 0.89    182.9   182.62  0.89    267.87  264.79  6.49    256.87  250.23  13.27   219.16  217.08  29.48   15.19   13.6    4.22
-26 965.89  969.6   8.54    996.89  998.45  5.47    326.95  329.26  9.33    345.86  338.48  15.18   318.64  315.39  17.52   309.46  324.8   34.46   1.75    1.74    0.13
+1  368.31  368.31  3.72    118.62  118.62  4.11    519.34  519.34  2.77    200.16  200.16  19.18   51.5    51.5    4.07    106.52  106.52  2.0 13.9    13.9    1.15
+2  577.57  579.63  14.26   298.11  287.69  25.04   401.62  403.49  5.56    108.92  119.52  20.26   175.46  148.48  49.99   266.93  204.28  136.79  0.75    0.41    0.59
+3  378.45  377.92  17.49   133.58  120.33  31.7    405.96  363.08  92.9    82.6    79.58   15.37   605.09  598.98  26.19   326.67  262.6   136.73  3.68    0.25    6.11
+4  373.1   369.15  20.1    210.01  216.15  40.09   93.28   91.46   20.61   204.97  195.61  62.67   104.63  103.22  3.66    358.35  299.58  149.23  2.37    1.06    2.9
+5  328.35  329.84  7.36    162.69  153.4   17.04   64.32   66.48   9.1 95.3    100.08  21.11   87.1    75.53   29.03   138.21  111.41  51.91   4.2 5.54    3.46
+6  368.41  369.04  11.26   150.35  148.67  20.18   72.04   69.0    6.23    102.47  96.05   30.23   610.15  608.79  2.45    266.72  240.66  45.65   6.19    3.08    6.59
+7  395.98  405.23  23.06   169.98  178.92  16.38   86.97   94.51   14.15   270.33  281.53  66.6    619.84  620.49  3.64    303.61  275.01  62.14   3.11    2.94    0.95
+8  402.95  402.95  45.04   141.51  141.51  41.7    509.14  509.14  11.8    193.58  193.58  93.02   572.66  572.66  99.37   412.15  412.15  132.02  5.63    5.63    7.93
+9  439.49  431.34  21.29   367.28  354.81  160.26  311.97  356.44  161.34  652.5   767.62  216.65  440.1   474.29  124.44  625.38  645.66  56.62   0.51    0.16    0.67
+10 360.07  360.07  0.95    114.5   114.5   5.18    513.44  513.44  2.91    40.28   40.28   7.32    61.76   61.76   0.71    113.04  113.04  13.46   17.0    17.0    2.65

and also the numbers don't match (they are similar). I don't have the domain knowledge to decide whether we can just strip the additional lines and whether there is an element of stochasticity in process that would take us to compare the files by equivalent size or number of lines rather than being exact results.

[emily101-gif]

@emily101-gif I have fixed the galaxy issues of the tool, but the tests are currently not passing because the flowstat3 test files are not equivalent to what the tool is outputting. Currently output1.flowstat3 and output2.flowstat3 files have around 16 more lines than the outputs generated by the tools:

JobOutputsError: History item  different than expected, difference (using diff):
( /var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmp8VmHXbout1.flowstat3 v. /var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmpO7Fkyxout1.flowstat3 )
--- local_file
+++ history_data
@@ -1,27 +1,27 @@
 Population   FSC_mean    FSC_median  FSC_stdev   SSC_mean    SSC_median  SSC_stdev   CD4_mean    CD4_median  CD4_stdev   CCR7_mean   CCR7_median CCR7_stdev  CD8_mean    CD8_median  CD8_stdev   CCR3_mean   CCR3_median CCR3_stdev  Percentage_mean Percentage_median   Percentage_stdev
-1    362.36  362.36  2.03    115.66  115.66  4.69    520.22  520.22  2.1 187.01  187.01  8.0 49.3    49.3    1.43    71.62   71.62   6.22    9.53    9.53    0.92
-2    434.28  374.35  111.03  173.06  125.62  92.77   481.01  521.93  74.19   53.87   39.72   27.49   123.6   72.0    94.92   262.34  197.55  140.75  4.77    5.35    4.11
-3    387.79  395.7   23.62   130.91  119.3   27.93   435.9   410.23  67.59   74.72   69.3    9.68    600.1   585.6   29.27   329.66  275.2   135.27  3.65    0.15    6.14
-4    362.46  363.32  6.82    204.27  204.11  37.15   89.98   96.34   14.26   176.99  147.5   52.47   99.4    102.85  11.5    379.43  318.19  129.33  2.15    0.42    3.06
-5    325.38  320.36  10.17   160.67  155.29  19.56   59.04   56.73   12.13   89.3    81.95   21.59   86.04   73.35   29.85   138.09  112.25  52.08   3.85    4.61    3.27
-6    368.28  368.59  11.22   150.66  148.89  19.84   72.55   69.32   5.76    104.15  96.05   37.15   610.48  612.42  3.86    266.97  244.06  45.55   6.11    3.08    6.26
-7    396.63  403.26  20.5    168.46  176.59  16.14   87.66   94.51   12.08   279.23  281.53  86.3    621.35  620.71  1.55    304.29  274.19  61.37   3.9 2.99    1.61
-8    404.55  404.55  47.31   144.35  144.35  45.71   517.41  517.41  0.11    341.18  341.18  115.72  460.13  460.13  258.52  471.42  471.42  48.2    5.63    5.63    7.93
-9    411.14  431.34  58.13   304.59  331.2   81.01   255.21  292.9   108.35  576.55  562.5   181.39  376.48  302.14  136.76  558.62  616.89  126.67  0.5 0.18    0.68
-10   355.5   355.5   4.74    112.88  112.88  3.84    520.08  520.08  0.38    31.22   31.22   1.9 58.0    58.0    5.33    67.4    67.4    6.98    8.64    8.64    1.69
-11   388.08  388.08  10.53   168.48  168.48  47.07   104.65  104.65  27.37   274.21  274.21  231.97  638.98  638.98  51.13   538.17  538.17  51.43   4.54    4.54    6.28
-12   428.71  421.38  16.73   335.25  241.15  165.09  130.58  120.19  22.63   198.19  205.92  43.13   212.07  215.97  22.59   168.98  147.47  50.14   2.43    3.0 1.21
-13   421.73  423.08  14.71   183.94  195.44  42.68   437.73  405.31  69.88   414.28  421.76  139.69  610.61  615.38  23.29   289.5   289.23  16.72   3.73    0.19    6.24
-14   373.78  363.33  22.49   142.58  136.41  43.0    448.64  460.06  83.19   598.24  567.5   67.94   234.64  77.56   279.04  158.48  164.12  43.29   1.61    0.08    2.68
-15   369.71  361.32  20.31   147.49  118.97  54.51   306.98  301.48  35.15   122.87  109.52  49.72   115.48  71.4    78.14   148.68  117.17  67.47   1.09    1.42    0.74
-16   419.18  419.08  14.47   284.65  264.01  99.6    107.66  107.35  12.52   479.28  510.36  61.47   134.26  130.48  13.97   198.02  201.21  28.44   1.41    0.58    1.51
-17   472.22  462.0   27.16   267.49  196.73  134.04  485.32  512.67  55.91   591.9   588.96  124.73  284.97  357.2   145.9   346.39  284.33  116.55  0.55    0.12    0.84
-18   391.3   388.6   9.62    151.22  132.42  42.06   468.62  525.67  101.55  200.8   197.56  12.67   150.61  64.27   151.76  251.49  205.87  109.27  4.37    5.28    3.77
-19   954.49  948.66  16.08   990.53  979.64  20.85   494.76  496.89  16.58   627.61  649.92  62.61   526.51  498.02  54.65   525.11  507.34  59.97   0.55    0.48    0.14
-20   420.28  431.49  23.44   220.23  175.21  96.79   128.13  108.33  59.81   528.18  547.09  71.02   636.01  620.52  55.87   359.88  338.83  106.83  2.7 0.53    4.19
-21   611.37  612.66  8.09    969.24  967.97  7.2 141.84  140.47  2.77    223.33  220.24  7.11    223.8   216.74  15.51   183.19  176.15  32.07   14.7    14.78   1.9
-22   666.05  677.97  29.25   452.57  434.17  32.95   377.8   376.69  16.57   226.24  215.63  23.58   212.9   192.78  35.36   277.65  267.15  39.06   2.22    2.36    0.64
-23   546.68  550.94  8.1 989.48  988.58  2.38    361.98  358.59  13.74   472.15  469.96  9.68    381.26  366.78  27.25   438.45  411.62  57.08   1.72    1.77    0.32
-24   683.11  692.69  31.65   446.21  473.52  51.33   394.62  397.71  7.78    202.01  214.78  26.42   192.77  183.47  31.32   148.62  143.66  27.39   2.14    2.2 0.53
-25   727.79  726.15  4.62    1017.52 1017.01 0.89    182.9   182.62  0.89    267.87  264.79  6.49    256.87  250.23  13.27   219.16  217.08  29.48   15.19   13.6    4.22
-26   965.89  969.6   8.54    996.89  998.45  5.47    326.95  329.26  9.33    345.86  338.48  15.18   318.64  315.39  17.52   309.46  324.8   34.46   1.75    1.74    0.13
+1    368.31  368.31  3.72    118.62  118.62  4.11    519.34  519.34  2.77    200.16  200.16  19.18   51.5    51.5    4.07    106.52  106.52  2.0 13.9    13.9    1.15
+2    577.57  579.63  14.26   298.11  287.69  25.04   401.62  403.49  5.56    108.92  119.52  20.26   175.46  148.48  49.99   266.93  204.28  136.79  0.75    0.41    0.59
+3    378.45  377.92  17.49   133.58  120.33  31.7    405.96  363.08  92.9    82.6    79.58   15.37   605.09  598.98  26.19   326.67  262.6   136.73  3.68    0.25    6.11
+4    373.1   369.15  20.1    210.01  216.15  40.09   93.28   91.46   20.61   204.97  195.61  62.67   104.63  103.22  3.66    358.35  299.58  149.23  2.37    1.06    2.9
+5    328.35  329.84  7.36    162.69  153.4   17.04   64.32   66.48   9.1 95.3    100.08  21.11   87.1    75.53   29.03   138.21  111.41  51.91   4.2 5.54    3.46
+6    368.41  369.04  11.26   150.35  148.67  20.18   72.04   69.0    6.23    102.47  96.05   30.23   610.15  608.79  2.45    266.72  240.66  45.65   6.19    3.08    6.59
+7    395.98  405.23  23.06   169.98  178.92  16.38   86.97   94.51   14.15   270.33  281.53  66.6    619.84  620.49  3.64    303.61  275.01  62.14   3.11    2.94    0.95
+8    402.95  402.95  45.04   141.51  141.51  41.7    509.14  509.14  11.8    193.58  193.58  93.02   572.66  572.66  99.37   412.15  412.15  132.02  5.63    5.63    7.93
+9    439.49  431.34  21.29   367.28  354.81  160.26  311.97  356.44  161.34  652.5   767.62  216.65  440.1   474.29  124.44  625.38  645.66  56.62   0.51    0.16    0.67
+10   360.07  360.07  0.95    114.5   114.5   5.18    513.44  513.44  2.91    40.28   40.28   7.32    61.76   61.76   0.71    113.04  113.04  13.46   17.0    17.0    2.65

and also the numbers don't match (they are similar). I don't have the domain knowledge to decide whether we can just strip the additional lines and whether there is an element of stochasticity in process that would take us to compare the files by equivalent size or number of lines rather than being exact results.

@pcm32 Strangely when I do the first test run in planemo - the flowsom mapping tool produces the same output as in the test file. The values appear to be exactly the same and have the same number of lines. It's really strange that yours is showing negative populations (and even more negative populations than there are positive). There is also no stochasticity in this tool. It is just summarising the results of FlowSOM and adding the results to the same FCS files used for the flowSOM.

planemo output::::: Population FSC_mean FSC_median FSC_stdev SSC_mean SSC_median SSC_stdev CD4_mean CD4_median CD4_stdev CCR3_mean CCR3_median CCR3_stdev CD8_mean CD8_median CD8_stdev CCR7_mean CCR7_median CCR7_stdev Percentage_mean Percentage_median Percentage_stdev 1 449.517033333333 417.6756 80.0730653843309 459.103833333333 390.0447 216.073684871165 39.8154533333333 40.13677 5.01452185878507 150.838 150.4859 38.395660843512 250.793593333333 284.0427 67.111722169429 167.260033333333 164.4792 32.347821647266 7.02 7.275 5.25714038237519 2 399.186966666667 394.1149 10.9973232744761 238.146333333333 249.3538 37.7163583478487 63.80977 55.70256 19.0417661339252 184.419233333333 158.2486 77.9796674462217 491.019236666667 521.78231 57.0066099143251 401.375833333333 357.4974 109.343631419042 7.67666666666667 2.205 10.5603389307983 3 467.2606 467.2606 62.422538115011 229.3288 229.3288 7.17175981750645 180.70303 180.70303 62.3625330335595 531.77725 531.77725 128.442764822021 687.00605 687.00605 95.8751235368435 776.07575 776.07575 7.17819448921528 0.1775 0.1775 0.215667568261897 4 491.897133333333 409.0643 149.780851176121 278.052733333333 184.868 168.832454839268 448.970486666667 476.89881 53.4724893652207 158.223133333333 167.6959 37.8623778168162 113.65597 71.6557 73.6871838168124 165.000733333333 136.2907 69.3533555861815 28.3566666666667 37.7 22.1368343114668 5 516.3916 490.4522 70.6730826772824 564.707533333333 496.6552 221.791228156961 217.89667 148.68824 136.239830947248 155.259766666667 151.626 26.5492160965881 386.466533333333 400.36621 119.854921059911 258.248033333333 210.7229 118.202621439304 20.925 21.04 10.7479614346163 6 503.986666666667 544.9372 91.1725446226732 529.892566666667 588.058 286.9690970419 66.6792266666667 68.47826 17.2981163164355 379.999266666667 363.4541 61.4031448561337 359.096546666667 354.7923 138.223751503987 222.893833333333 240.6476 33.605210605847 3.45666666666667 1.035 4.51866776089295 7 543.537233333333 560.5087 42.3007222355994 656.858366666667 727.4167 153.183832006003 162.490643333333 120.46087 73.4431415786262 337.339266666667 313.5 69.0314434588567 117.343473333333 128.84783 25.6863284384793 154.5796 152.2522 13.606813291877 1.55333333333333 1.15 1.49633997919368 8 637.9505 629.9274 49.7939072153411 803.6457 786.0875 145.730875121197 254.312376666667 225.76559 58.7006535935217 325.855566666667 335.3947 23.430565280704 338.334176666667 319.91354 68.775726534905 252.833433333333 239.1529 43.9294104988143 29.25 27.815 11.9174735158086 9 713.288166666667 727.5 183.065256728641 653.217366666667 731 248.41473494695 462.796183333333 530.46667 211.3275442529 834.4092 870.5 72.4875762589011 714.039573333333 614.71875 210.964602501457 670.178633333333 604.3667 275.704133227076 0.273333333333333 0.15 0.32316146634977 10 470.2887 463.1167 45.1998847698753 375.647433333333 305.7 202.644669803485 169.1044 132.08403 67.2489033808351 592.7282 610.3137 35.3658586669404 284.34763 252.89583 110.968356521537 255.033566666667 243.4132 29.0586790013471 1.37 0.3 1.90549206243427

Test-data output:::: Population FSC_mean FSC_median FSC_stdev SSC_mean SSC_median SSC_stdev CD4_mean CD4_median CD4_stdev CCR3_mean CCR3_median CCR3_stdev CD8_mean CD8_median CD8_stdev CCR7_mean CCR7_median CCR7_stdev Percentage_mean Percentage_median Percentage_stdev 1 449.517033333333 417.6756 80.0730653843309 459.103833333333 390.0447 216.073684871165 39.8154533333333 40.13677 5.01452185878507 150.838 150.4859 38.395660843512 250.793593333333 284.0427 67.111722169429 167.260033333333 164.4792 32.347821647266 7.02 7.275 5.25714038237519 2 399.186966666667 394.1149 10.9973232744761 238.146333333333 249.3538 37.7163583478487 63.80977 55.70256 19.0417661339252 184.419233333333 158.2486 77.9796674462217 491.019236666667 521.78231 57.0066099143251 401.375833333333 357.4974 109.343631419042 7.67666666666667 2.205 10.5603389307983 3 467.2606 467.2606 62.422538115011 229.3288 229.3288 7.17175981750645 180.70303 180.70303 62.3625330335595 531.77725 531.77725 128.442764822021 687.00605 687.00605 95.8751235368435 776.07575 776.07575 7.17819448921528 0.1775 0.1775 0.215667568261897 4 491.897133333333 409.0643 149.780851176121 278.052733333333 184.868 168.832454839268 448.970486666667 476.89881 53.4724893652207 158.223133333333 167.6959 37.8623778168162 113.65597 71.6557 73.6871838168124 165.000733333333 136.2907 69.3533555861815 28.3566666666667 37.7 22.1368343114668 5 516.3916 490.4522 70.6730826772824 564.707533333333 496.6552 221.791228156961 217.89667 148.68824 136.239830947248 155.259766666667 151.626 26.5492160965881 386.466533333333 400.36621 119.854921059911 258.248033333333 210.7229 118.202621439304 20.925 21.04 10.7479614346163 6 503.986666666667 544.9372 91.1725446226732 529.892566666667 588.058 286.9690970419 66.6792266666667 68.47826 17.2981163164355 379.999266666667 363.4541 61.4031448561337 359.096546666667 354.7923 138.223751503987 222.893833333333 240.6476 33.605210605847 3.45666666666667 1.035 4.51866776089295 7 543.537233333333 560.5087 42.3007222355994 656.858366666667 727.4167 153.183832006003 162.490643333333 120.46087 73.4431415786262 337.339266666667 313.5 69.0314434588567 117.343473333333 128.84783 25.6863284384793 154.5796 152.2522 13.606813291877 1.55333333333333 1.15 1.49633997919368 8 637.9505 629.9274 49.7939072153411 803.6457 786.0875 145.730875121197 254.312376666667 225.76559 58.7006535935217 325.855566666667 335.3947 23.430565280704 338.334176666667 319.91354 68.775726534905 252.833433333333 239.1529 43.9294104988143 29.25 27.815 11.9174735158086 9 713.288166666667 727.5 183.065256728641 653.217366666667 731 248.41473494695 462.796183333333 530.46667 211.3275442529 834.4092 870.5 72.4875762589011 714.039573333333 614.71875 210.964602501457 670.178633333333 604.3667 275.704133227076 0.273333333333333 0.15 0.32316146634977 10 470.2887 463.1167 45.1998847698753 375.647433333333 305.7 202.644669803485 169.1044 132.08403 67.2489033808351 592.7282 610.3137 35.3658586669404 284.34763 252.89583 110.968356521537 255.033566666667 243.4132 29.0586790013471 1.37 0.3 1.90549206243427

[pcm32]

@emily101-gif the initial line with a - or + is the diff showing you the two different files. The second set of lines (pluses) is the result of the test run, the minuses is the content of the file given in the test data directory (test-data/run1 and run2). So the files there don't match either what you got as result.

[emily101-gif]

@emily101-gif the initial line with a - or + is the diff showing you the two different files. The second set of lines (pluses) is the result of the test run, the minuses is the content of the file given in the test data directory (test-data/run1 and run2). So the files there don't match either what you got as result.

OK well if you're happy with me doing so then I can change the output files to the ones we are getting - as the tool seems to be working. It could be that there were some errors with the test files which were never checked as it was not pushed to the toolshed?

[pcm32]

Yes, if you are satisfied with what the tool does, then let's change the expected results file.

[emily101-gif]

Yes, if you are satisfied with what the tool does, then let's change the expected results file.

Great I will change it now.

[emily101-gif]

Hi Pablo. I've just noticed that the tool on this branch doesn't appear to be updated to the same point as the master. The tool repository on this branch doesn't contain the R code and therefore the XML file doesn't link to the script within the tool repo. Just wondering if this was deliberate? @pcm32

[pcm32]

@emily101-gif to which R code do you refer? If you look at the changes of the PR, there is no R code deletion as far as I can see. The python code doesn't call any R code either, besides cent_adjust (not sure if this is R), which is provided by the flock dependency AFAIK. Maybe if you paste links to the R code that you mean? What particular differences do you see with master? Again, they would be reflected in the PR changes here. Or do you mean a different git repository, such as immport-galaxy main repo?

[emily101-gif]

Really sorry I think I was looking at the wrong tool (on my previous comment about missing R script)!

I'm still getting the same outputs for the flowstat3 files for both runs though and I get no output when I run diff on the two files. I have attached them below as txt files so they could be loaded into Github for you to see. Therefore, I don't think there is much point me changing the flowstat3 example output files as they would be the same as the ones I'm getting. The only other I can think is that it could be due to the order of the output files in the tag: flowstat3 comes before flowstat2 - but they are named and I would ealso xpect an error to also be occurring with flowstat2 ... @pcm32

run1:

flowstat3 expected output: out1.txt

flowstat3 output from running in planemo Galaxy13-[mfi_descriptive_stats_of_CrossSample_on_list_using_mfi].txt

run2:

flowstat3 expected output: out2.txt

flowstats3 outcome from running in planemo: Galaxy44-[gmfi_descriptive_stats_of_CrossSample_on_list_using_gmfi].txt

[pcm32]

Tests are passing, maybe my local branch was dirty somehow.