Mercurial > repos > iuc > fargene

changeset 1:239ce9f24386 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit 0b2de0d35b6ef4c0ef0dd77e8415115a4a3b415b"
author iuc
date Mon, 02 Dec 2019 04:39:18 -0500
parents 6f743c615c41
children b982a9ea939c
files fargene.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fargene.xml	Thu Nov 28 14:39:41 2019 -0500
+++ b/fargene.xml	Mon Dec 02 04:39:18 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="fargene" name="fargene" version="@VERSION@">
+<tool id="fargene" name="fargene" version="@VERSION@+galaxy1">
     <description>Fragmented antibiotic resistance gene identifier </description>
     <macros>
         <import>macros.xml</import>
@@ -70,7 +70,7 @@
     #end if
     &&
     #if $inputs.input_type in ('paired', 'collection'):
-        tar czf retrievedFragments.tar.gz fargene_output/retrievedFragments
+        tar -czf retrievedFragments.tar.gz fargene_output/retrievedFragments
     #end if
     2>&1
     ]]>    </command>
@@ -131,10 +131,10 @@
         <data name="fargene_log" format="txt" from_work_dir="fargene_analysis.log" label="${tool.name} on ${on_string} (log)">
         </data>
         <collection name="hmmsearchresults" type="list" label="HMM Search Result">
-            <discover_datasets pattern="__name__" directory="fargene_output/hmmsearchresults" format="txt" ext="out" visible="false" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+).out" directory="fargene_output/hmmsearchresults" format="txt" visible="false" />
         </collection>
         <collection name="predictedGenes" type="list" label="Predicted Genes">
-            <discover_datasets pattern="__name__" directory="fargene_output/predictedGenes" ext="fasta" format="fasta" visible="false" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+).fasta" directory="fargene_output/predictedGenes" format="fasta" visible="false" />
         </collection>
     </outputs>
     <tests>
--- a/macros.xml	Thu Nov 28 14:39:41 2019 -0500
+++ b/macros.xml	Mon Dec 02 04:39:18 2019 -0500
@@ -2,7 +2,8 @@
     <token name="@VERSION@">0.1</token>
     <xml name="requirements">
         <requirements>
-        <requirement type="package" version="@VERSION@">fargene</requirement>
+            <requirement type="package" version="@VERSION@">fargene</requirement>
+            <requirement type="package" version="1.32">tar</requirement>
             <yield/>
         </requirements>
     </xml>