Mercurial > repos > iracooke > tpp_prophets
changeset 16:1b86e378de37 draft
Fix tabular outputs. Export XML_ONLY variable
| author | iracooke |
|---|---|
| date | Mon, 26 Oct 2015 20:40:34 -0400 |
| parents | 0746a2ae9e04 |
| children | 868e75fc0f70 |
| files | interprophet.xml peptide_prophet.xml pepxml_to_table.xml tool_dependencies.xml |
| diffstat | 4 files changed, 8 insertions(+), 2 deletions(-) [+] |
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--- a/interprophet.xml Tue Oct 20 20:45:24 2015 -0400 +++ b/interprophet.xml Mon Oct 26 20:40:34 2015 -0400 @@ -7,6 +7,8 @@ </requirements> <command> <![CDATA[ + export XML_ONLY="true"; + interprophet.rb --galaxy #if str( $input_type.type ) == "files": #for $pepxml_file in $input_type.pepxml_files:
--- a/peptide_prophet.xml Tue Oct 20 20:45:24 2015 -0400 +++ b/peptide_prophet.xml Mon Oct 26 20:40:34 2015 -0400 @@ -6,6 +6,10 @@ <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> </requirements> <command> + # This should be in the tpp_package. + # A hack for now + export XML_ONLY="true"; + peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml
--- a/pepxml_to_table.xml Tue Oct 20 20:45:24 2015 -0400 +++ b/pepxml_to_table.xml Mon Oct 26 20:40:34 2015 -0400 @@ -11,7 +11,7 @@ <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> </inputs> <outputs> - <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> + <data format="tabular" name="output" metadata_source="input_file" label="${input_file.display_name}.tsv" /> </outputs> <tests> <!-- Just test that the tool runs and produces vaguely correct output -->
--- a/tool_dependencies.xml Tue Oct 20 20:45:24 2015 -0400 +++ b/tool_dependencies.xml Mon Oct 26 20:40:34 2015 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="protk" version="1.4.3"> - <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="991797b02976" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="trans_proteomic_pipeline" version="4.8.0"> <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />