diff pep_match.xml @ 2:bf6acfb148a8 draft default tip

planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper commit 040d09319fb0f43fafb1d3ebd99af41bce0f6bfd

--- a/pep_match.xml	Mon Dec 13 14:12:43 2021 +0000
+++ b/pep_match.xml	Thu Jul 18 10:26:43 2024 +0000
@@ -1,13 +1,13 @@
-<tool id="peptimapper_pep_match" name="PepMatch" version="2.0">
+<tool id="peptimapper_pep_match" name="PepMatch" version="2.1">
     <description>align PSTs on sequence and cluster hits</description>
     <requirements>
-        <container type="docker">dockerprotim/peptimapper</container>
+        <container type="docker">dockerprotim/peptimapper@sha256:d3eb807d7d5aa155f7b39d05a47420e0a0a9191d5fa867b6ca1be763f8a23bf1</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 ln -s '$fastafile' 'in.fa' &&
 ln -s '$tagsfile' 'in.tags' &&
 LXRunPepMatch -D $D -t $t -T $T -d $d 'in.fa' 'in.tags' &&
-mv 'in.tags.in.fa.trans.${D}.hit' ${hitsfile} &&
+mv 'in.tags.in.fa.trans.${D}.hit' '${hitsfile}' &&
 mv 'in.tags.in.fa.trans.${D}.hit.${t}.${T}.${d}.clust' '${clustersfile}'
     ]]></command>
     <inputs>
@@ -15,7 +15,7 @@
         <param name="fastafile" type="data" format="fasta" label="Chromosome file (Fasta)" help="Chromosome file" />
 
         <param name="D" type="select" label="Mass tolerance" help="uma">
-            <option value="0.5" selected="selected">0.5</option>
+            <option value="0.5" selected="true">0.5</option>
             <option value="0.25">0.25</option>
             <option value="0.025">0.025</option>
             <option value="0.0025">0.0025</option>
@@ -23,13 +23,13 @@
         </param>
 
         <param name="t" type="select" label="Min. hits" help="Minimal hits number per cluster">
-            <option value="2" selected="selected">2</option>
+            <option value="2" selected="true">2</option>
             <option value="3">3</option>
             <option value="4">4</option>
         </param>
 
         <param name="T" type="select" label="Min. peptides" help="Minimal peptides number per cluster">
-            <option value="2" selected="selected">2</option>
+            <option value="2" selected="true">2</option>
             <option value="3">3</option>
             <option value="4">4</option>
         </param>
@@ -38,7 +38,7 @@
             <option value="500">500</option>
             <option value="1000">1000</option>
             <option value="2000">2000</option>
-            <option value="5000" selected="selected">5000</option>
+            <option value="5000" selected="true">5000</option>
             <option value="10000">10000</option>
             <option value="15000">15000</option>
             <option value="20000">20000</option>