Mercurial > repos > galaxyp > myrimatch
changeset 6:7ba6c7b12b30 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/myrimatch commit 9eee537ea6d1e33b21596390767e7701f95a67d3
author | galaxyp |
---|---|
date | Wed, 01 Feb 2017 20:53:11 -0500 |
parents | caf7e9d77981 |
children | d0327187b97e |
files | macros.xml myrimatch.xml |
diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/macros.xml Tue Dec 13 11:27:46 2016 -0500 +++ b/macros.xml Wed Feb 01 20:53:11 2017 -0500 @@ -1,8 +1,8 @@ <macros> - <token name="@VERSION@">3.0.10158</token> + <token name="@VERSION@">3.0.10246</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3_0_10158">bumbershoot</requirement> + <requirement type="package" version="3_0_10246">bumbershoot</requirement> <yield/> </requirements> </xml>
--- a/myrimatch.xml Tue Dec 13 11:27:46 2016 -0500 +++ b/myrimatch.xml Wed Feb 01 20:53:11 2017 -0500 @@ -13,7 +13,7 @@ <command> <![CDATA[ #set $db_name = $ProteinDatabase.display_name.replace(".fasta", "") + ".fasta" - #if $OutputFormat.value == "mzid" + #if $OutputFormat.value == "mzIdentML" #set $output_ext="mzid" #else #set $output_ext="pepXML" @@ -75,7 +75,7 @@ <param name="input" type="data" format="mzml,mzxml,mgf,ms2,mz5" label="Input Raw MS File(s)"/> <param argument="-OutputFormat" type="select" label="Output Type" help="The file format to use for results of the search."> <option value="pepXML">pepXML</option> - <option value="mzid">mzIdentML</option> + <option value="mzIdentML">mzIdentML</option> </param> <param argument="-ProteinDatabase" format="fasta" type="data" label="Protein Database" help="The FASTA protein database to search against. Only amino-acid type FASTA is supported." /> <param argument="-DecoyPrefix" type="text" label="Decoy Prefix" value="rev_" help="If the protein database contains accessions prefixed with this string, those proteins will be considered decoys. If there are no decoy protein, this prefix will be used to generate an automatic decoy for each target protein. Set this to an empty string to disable automatic decoys." /> @@ -181,7 +181,7 @@ <outputs> <data format="raw_pepxml" name="output" from_work_dir="output"> <change_format> - <when input="OutputFormat" value="mzid" format="mzid" /> + <when input="OutputFormat" value="mzIdentML" format="mzid" /> </change_format> </data> </outputs> @@ -207,7 +207,7 @@ <param name="MaxResultRank" value="3" /> <param name="MonoisotopeAdjustmentSet" value="[-1,2]" /> <param name="UseSmartPlusThreeModel" value="false" /> - <output name="output" file="201208-378803-mm.pepXML" lines_diff="12" /> + <output name="output" file="201208-378803-mm.pepXML" lines_diff="14" /> </test> <test> <param name="input" value="input/201208-378803.mzML" /> @@ -221,7 +221,7 @@ <param name="NumChargeStates" value="3" /> <param name="MaxResultRank" value="1" /> <param name="MonoisotopeAdjustmentSet" value="0" /> - <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="12" /> + <output name="output" file="201208-378803-mm-15ppm-fully-tryptic.pepXML" lines_diff="14" /> </test> </tests> <help>