Mercurial > repos > iuc > bioext_bam2msa

diff bam2msa.xml @ 2:0a4ad829d87a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit b8438e86497e5f1084cca1c9b2fdc82c80a7e1b0"
author iuc
date Fri, 09 Jul 2021 15:18:46 +0000
parents 12729213b4ae
children b226e0c805a5
line wrap: on
line diff
--- a/bam2msa.xml	Thu May 13 16:57:46 2021 +0000
+++ b/bam2msa.xml	Fri Jul 09 15:18:46 2021 +0000
@@ -1,35 +1,36 @@
 <?xml version="1.0"?>
-<tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
-  <description>to FASTA multiple sequence alignment</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <command detect_errors="exit_code"><![CDATA[
-    bam2msa
-        #if $region_start and $region_end:
-            -r $region_start:$region_end
-        #end if
-        '$input' '$output'
-    ]]></command>
-  <inputs>
-    <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
-    <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
-    <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
-  </inputs>
-  <outputs>
-    <data name="output" format="fasta"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" ftype="bam" value="bealign-out1.bam"/>
-      <output name="output" file="bam2msa-out1.fa"/>
-    </test>
-    <test>
-      <param name="input" ftype="bam" value="bealign-out2.bam"/>
-      <output name="output" file="bam2msa-out2.fa"/>
-    </test>
-  </tests>
-  <help>Extract MSA from a BAM file</help>
-  <expand macro="citations"/>
+<tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>to FASTA multiple sequence alignment</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        bam2msa
+            #if $region_start and $region_end:
+                -r $region_start:$region_end
+            #end if
+            '$input' '$output'
+        ]]></command>
+    <inputs>
+        <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
+        <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
+        <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="bam" value="bealign-out1.bam"/>
+            <output name="output" file="bam2msa-out1.fa"/>
+        </test>
+        <test>
+            <param name="input" ftype="bam" value="bealign-out2.bam"/>
+            <output name="output" file="bam2msa-out2.fa"/>
+        </test>
+    </tests>
+    <help>Extract MSA from a BAM file</help>
+    <expand macro="citations"/>
 </tool>