Mercurial > repos > jjohnson > encyclopedia_quantify
changeset 3:aa52f0eadc85 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 96a023cccea27c30ff61caf271a3c79b92db1873"
| author | jjohnson |
|---|---|
| date | Tue, 07 Jul 2020 11:56:28 -0400 |
| parents | 174886084dc5 |
| children | bd937e4efa04 |
| files | encyclopedia_quantify.xml macros.xml |
| diffstat | 2 files changed, 21 insertions(+), 7 deletions(-) [+] |
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--- a/encyclopedia_quantify.xml Thu Jul 02 11:07:46 2020 -0400 +++ b/encyclopedia_quantify.xml Tue Jul 07 11:56:28 2020 -0400 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ @CMD_IMPORTS@ @LINK_SCAN_INPUTS@ @LINK_FASTA_INPUT@ @@ -25,6 +25,7 @@ @MODIFICATION_OPTIONS@ @SEARCH_OPTIONS@ | tee -a search2lib.log ; done && + for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \$TXT | sed 's/mzML/dia/'`; ln -s \$TXT \$TRGT; done && EncyclopeDIA -Djava.awt.headless=true -Xmx12g -libexport @SCAN_INPUTS@ @FASTA_INPUT@ @@ -32,6 +33,7 @@ @LIB_INPUT@ -a $a -o chromatogram_library.elib + && ls -l ./*.* inputs/* | tee -a search2lib.log ]]></command> <inputs> @@ -47,6 +49,10 @@ <option value="features" selected="true">concatenated_features.txt</option> <option value="results" selected="true">concatenated_results.txt</option> <option value="decoy" selected="false">concatenated_decoy.txt</option> + <!-- + <option value="rt_plots" selected="false">Retention Time Plots</option> + <option value="rt_tables" selected="false">Retention Time Tables</option> + --> <option value="peptides" selected="true">peptides.txt (requires align between files)</option> <option value="proteins" selected="true">proteins.txt (requires align between files)</option> </param> @@ -76,13 +82,23 @@ <action name="column_names" type="metadata" default="PSMId,score,q-value,posterior_error_prob,peptide,proteinIds" /> </actions> </data> - <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.peptides.txt"> + <!-- + <collection name="rt_plots" type="list" label="${tool.name} - ${on_string}: Retention Time Plots"> + <filter>l and 'rt_plots' in select_outputs</filter> + <discover_datasets pattern="(?P<designation>.+\.pdf)" ext="pdf" directory="inputs"/> + </collection> + <collection name="rt_tables" type="list" label="${tool.name} - ${on_string}: Retention Time Tables"> + <filter>l and 'rt_tables' in select_outputs</filter> + <discover_datasets pattern="(?P<designation>.+\.rt_fit\.txt)" ext="tabular" directory="inputs"/> + </collection> + --> + <data name="peptides" format="tabular" label="${tool.name} ${on_string} peptides.txt" from_work_dir="chromatogram_library.elib.peptides.txt"> <filter>a and 'peptides' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Peptide,Protein,numFragments" /> </actions> </data> - <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.proteins.txt"> + <data name="proteins" format="tabular" label="${tool.name} ${on_string} proteins.txt" from_work_dir="chromatogram_library.elib.proteins.txt"> <filter>a and 'proteins' in select_outputs</filter> <actions> <action name="column_names" type="metadata" default="Protein,NumPeptides,PeptideSequences" />
--- a/macros.xml Thu Jul 02 11:07:46 2020 -0400 +++ b/macros.xml Tue Jul 07 11:56:28 2020 -0400 @@ -31,14 +31,12 @@ #end if #end def #def clean($name1) - ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i[.](fa|fasta|imzml|mzml)$)','', $re.sub('.*/','', $name1.rstrip('.gz')))) - ## #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('.*/','', $name1.rstrip('.gz'))) - #set $name_clean = $re.sub('[^\w\-_\.]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fasta|imzml|mzml)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) #return $name_clean #end def #def ln_name($ds) #set $ext = '' - #if $ds.is_of_type('mzml') + #if $ds.is_of_type('mzml') or $ds.is_of_type('imzml') #set $ext = ".mzML" #else if $ds.is_of_type('elib') #set $ext = ".elib"