| Previous changeset 1:b1fa45bd2b44 (2017-05-02) Next changeset 3:cfd7c4aa5c26 (2020-01-03) |
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Commit message:
Uploaded |
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modified:
GalFilter/generic_filter.xml |
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added:
GalFilter/.shed.yml GalFilter/.travis.yml GalFilter/planemo_test.sh GalFilter/test-data/in_DM1.tabular GalFilter/test-data/in_SM1.tabular GalFilter/test-data/in_VM1.tabular GalFilter/test-data/out_DM1.tabular GalFilter/test-data/out_SM1.tabular GalFilter/test-data/out_VM1.tabular |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/.shed.yml Tue Jun 27 05:57:04 2017 -0400 |
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| @@ -0,0 +1,9 @@ +categories: [Metabolomics] +description: '[W4M][Utils] Filtering according to specific variables' +homepage_url: http://workflow4metabolomics.org +long_description: 'Part of the W4M project: http://workflow4metabolomics.org / The + R script removes all samples and/or variables corresponding to specific values + regarding designated factors or numerical variables, in datasets corresponding to + dataMatrix, sampleMetadata and variableMetadata.' +name: generic_filter +owner: melpetera |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/.travis.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/.travis.yml Tue Jun 27 05:57:04 2017 -0400 |
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| @@ -0,0 +1,19 @@ +# This is a special configuration file to run tests on Travis-CI via +# GitHub notifications when changes are committed. +# +# See http://travis-ci.org/ for details +language: python + +before_install: + - sudo apt-get install -y python-virtualenv + - virtualenv planemo-venv + - . planemo-venv/bin/activate + - pip install --upgrade pip setuptools + - pip install planemo + - planemo conda_init + +install: + - planemo conda_install ${TRAVIS_BUILD_DIR} + +script: +- planemo test --install_galaxy --no_cache_galaxy --conda_dependency_resolution ${TRAVIS_BUILD_DIR} \ No newline at end of file |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/generic_filter.xml --- a/GalFilter/generic_filter.xml Tue May 02 04:49:24 2017 -0400 +++ b/GalFilter/generic_filter.xml Tue Jun 27 05:57:04 2017 -0400 |
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| @@ -1,7 +1,10 @@ -<tool id="generic_filter" name="Generic_Filter" version="2017.04"> +<tool id="generic_filter" name="Generic_Filter" version="2017.06"> <description>Removes elements according to numerical or qualitative values</description> - <command interpreter="Rscript"> - filter_wrap.R + <requirements> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + <command> + Rscript '$__tool_directory__/filter_wrap.R' dataMatrix_in "$dataMatrix_in" sampleMetadata_in "$sampleMetadata_in" variableMetadata_in "$variableMetadata_in" @@ -111,6 +114,30 @@ <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> </outputs> + <tests> + <test> + <param name="dataMatrix_in" value="in_DM1.tabular"/> + <param name="sampleMetadata_in" value="in_SM1.tabular"/> + <param name="variableMetadata_in" value="in_VM1.tabular"/> + <conditional name="numeric_condition"> + <param name="Factors" value="TRUE"/> + <param name="numeric_repeat_0|num_file" value="variable"/> + <param name="numeric_repeat_0|parm_col_num" value="rt"/> + <param name="numeric_repeat_0|interval_condition|interval" value="lower"/> + <param name="numeric_repeat_0|interval_condition|low_value" value="1.2"/> + </conditional> + <conditional name="qualitative_condition"> + <param name="Factors" value="TRUE"/> + <param name="qualitative_repeat_0|qual_file" value="sample"/> + <param name="qualitative_repeat_0|factor_col" value="Time"/> + <param name="qualitative_repeat_0|factors_value" value="3"/> + </conditional> + <output name="dataMatrix_out" file="out_DM1.tabular"/> + <output name="sampleMetadata_out" file="out_SM1.tabular"/> + <output name="variableMetadata_out" file="out_VM1.tabular"/> + </test> + </tests> + <help> .. class:: infomark @@ -254,4 +281,7 @@ Soon see the corresponding "Page" </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> </tool> \ No newline at end of file |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/planemo_test.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/planemo_test.sh Tue Jun 27 05:57:04 2017 -0400 |
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| @@ -0,0 +1,3 @@ +planemo conda_init --conda_prefix /tmp/mc/ +planemo conda_install --conda_prefix /tmp/mc/ . +planemo test --install_galaxy --conda_dependency_resolution --conda_prefix /tmp/mc/ --no_cleanup \ No newline at end of file |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/in_DM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/in_DM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
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| b'@@ -0,0 +1,746 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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/in_SM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/in_SM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
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| @@ -0,0 +1,50 @@ +sampleMetadata batch injectionOrder sampleType Time Group +Sample1 s1 2 sample 1 A +Sample2 s1 3 sample 2 B +Sample3 s1 17 sample 4 C +Sample4 s1 20 sample 3 B +Sample5 s1 47 sample 1 A +Sample6 s1 48 sample 2 B +Sample7 s2 59 sample 4 A +Sample8 s2 64 sample 2 C +Sample9 s2 86 sample 4 C +Sample10 s2 87 sample 1 A +Sample11 s2 96 sample 3 B +Sample12 s2 97 sample 1 C +Sample13 s3 105 sample 2 B +Sample14 s3 106 sample 4 A +Sample15 s3 107 sample 3 D +Sample16 s3 113 sample 1 A +Sample17 s3 114 sample 2 C +Sample18 s3 120 sample 1 B +Sample19 s3 126 sample 4 A +Sample20 s4 155 sample 2 B +Sample21 s4 158 sample 1 C +Sample22 s4 159 sample 3 A +Sample23 s4 171 sample 4 B +Sample24 s4 172 sample 2 A +Sample25 s4 173 sample 1 C +Sample26 s4 177 sample 4 F +Sample27 s4 178 sample 1 F +Sample28 s4 181 sample 2 F +Sample29 s4 182 sample 3 F +Sample30 s2 52 pool 5 E +Sample31 s2 63 pool 5 E +Sample32 s2 83 pool 5 E +Sample33 s2 93 pool 5 E +Sample34 s2 102 pool 5 E +Sample35 s3 103 pool 5 E +Sample36 s3 112 pool 5 E +Sample37 s3 132 pool 5 E +Sample38 s3 143 pool 5 E +Sample39 s3 152 pool 5 E +Sample40 s4 163 pool 5 E +Sample41 s4 174 pool 5 E +Sample42 s4 185 pool 5 E +Sample43 s4 196 pool 5 E +Sample44 s1 1 pool 5 E +Sample45 s1 11 pool 5 E +Sample46 s1 22 pool 5 E +Sample47 s1 28 pool 5 E +Sample48 s1 39 pool 5 E +Sample49 s1 51 pool 5 E |
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| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/in_VM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/in_VM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
| b |
| b'@@ -0,0 +1,746 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|
| b |
| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/out_DM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/out_DM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
| b |
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|
| b |
| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/out_SM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/out_SM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
| b |
| @@ -0,0 +1,45 @@ +sampleMetadata batch injectionOrder sampleType Time Group +Sample1 s1 2 sample 1 A +Sample2 s1 3 sample 2 B +Sample3 s1 17 sample 4 C +Sample5 s1 47 sample 1 A +Sample6 s1 48 sample 2 B +Sample7 s2 59 sample 4 A +Sample8 s2 64 sample 2 C +Sample9 s2 86 sample 4 C +Sample10 s2 87 sample 1 A +Sample12 s2 97 sample 1 C +Sample13 s3 105 sample 2 B +Sample14 s3 106 sample 4 A +Sample16 s3 113 sample 1 A +Sample17 s3 114 sample 2 C +Sample18 s3 120 sample 1 B +Sample19 s3 126 sample 4 A +Sample20 s4 155 sample 2 B +Sample21 s4 158 sample 1 C +Sample23 s4 171 sample 4 B +Sample24 s4 172 sample 2 A +Sample25 s4 173 sample 1 C +Sample26 s4 177 sample 4 F +Sample27 s4 178 sample 1 F +Sample28 s4 181 sample 2 F +Sample30 s2 52 pool 5 E +Sample31 s2 63 pool 5 E +Sample32 s2 83 pool 5 E +Sample33 s2 93 pool 5 E +Sample34 s2 102 pool 5 E +Sample35 s3 103 pool 5 E +Sample36 s3 112 pool 5 E +Sample37 s3 132 pool 5 E +Sample38 s3 143 pool 5 E +Sample39 s3 152 pool 5 E +Sample40 s4 163 pool 5 E +Sample41 s4 174 pool 5 E +Sample42 s4 185 pool 5 E +Sample43 s4 196 pool 5 E +Sample44 s1 1 pool 5 E +Sample45 s1 11 pool 5 E +Sample46 s1 22 pool 5 E +Sample47 s1 28 pool 5 E +Sample48 s1 39 pool 5 E +Sample49 s1 51 pool 5 E |
| b |
| diff -r b1fa45bd2b44 -r 12cf1eed21f4 GalFilter/test-data/out_VM1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GalFilter/test-data/out_VM1.tabular Tue Jun 27 05:57:04 2017 -0400 |
| b |
| b'@@ -0,0 +1,691 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