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changeset 6:7ba6c7b12b30 draft

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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(-) [+]
line wrap: on
line diff
--- 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>