Mercurial > repos > galaxyp > encyclopedia_fasta_to_prosit_csv
changeset 2:b2ae586dc13b draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34
| author | galaxyp |
|---|---|
| date | Tue, 17 May 2022 14:54:48 +0000 |
| parents | 469da8c03202 |
| children | |
| files | encyclopedia_fasta_to_prosit_csv.xml macros.xml |
| diffstat | 2 files changed, 20 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/encyclopedia_fasta_to_prosit_csv.xml Thu Apr 08 17:55:16 2021 +0000 +++ b/encyclopedia_fasta_to_prosit_csv.xml Tue May 17 14:54:48 2022 +0000 @@ -4,7 +4,7 @@ <import>macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="aggressive"><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ EncyclopeDIA -convert -fastatoprositcsv -i '$i' -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
--- a/macros.xml Thu Apr 08 17:55:16 2021 +0000 +++ b/macros.xml Tue May 17 14:54:48 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.2</token> + <token name="@TOOL_VERSION@">1.12.34</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -293,16 +293,21 @@ </param> <when value="no"/> <when value="yes"> - <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/> - <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/> - <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/> + <param argument="-percolatorVersion" type="text" value="3.01" optional="true" label="percolatorVersion"> + <option value="2.10">2.10</option> + <option value="3.01">3.01</option> + <option value="3.05">3.05</option> + <validator type="regex" message="Not percolator version format">^\d([.]\d+)?$</validator> + </param> + <param argument="-percolatorProteinThreshold" type="float" value="0.01" optional="true" label="percolatorProteinThreshold"/> + <param argument="-percolatorThreshold" type="float" value="0.01" optional="true" label="percolatorThreshold"/> </when> </conditional> </xml> <token name="@PERCOLATOR_OPTIONS@"> #if $options.percolator.set_percolator == 'yes' - #if str($options.percolator.percolatorVersionNumber) - -percolatorVersionNumber $options.percolator.percolatorVersionNumber + #if str($options.percolator.percolatorVersion) + -percolatorVersion $options.percolator.percolatorVersion #end if #if str($options.percolator.percolatorProteinThreshold) -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold @@ -310,6 +315,8 @@ #if str($options.percolator.percolatorThreshold) -percolatorThreshold $options.percolator.percolatorThreshold #end if + #else + -percolatorVersion "3.01" #end if </token> @@ -525,6 +532,12 @@ @FASTA_INPUT@ @TARGET_FASTA@ @LIB_INPUT@ + @MASS_LIBRARY_TOLERANCE@ + @PERCOLATOR_OPTIONS@ + @PEAK_OPTIONS@ + @WINDOW_OPTIONS@ + @MODIFICATION_OPTIONS@ + @SEARCH_OPTIONS@ -a $a -o chromatogram_library.elib && ls -l ./*.* inputs/*