diff chira_map.xml @ 17:7925dd016f53 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"

--- a/chira_map.xml	Fri Sep 24 06:50:39 2021 +0000
+++ b/chira_map.xml	Sun Dec 19 15:48:59 2021 +0000
@@ -1,9 +1,9 @@
-<tool id="chira_map" name="ChiRA map" version="@WRAPPER_VERSION@0">
+<tool id="chira_map" name="ChiRA map" version="@TOOL_VERSION@0">
     <description>map reads to trascriptome</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive"><![CDATA[
         chira_map.py -b
@@ -123,7 +123,6 @@
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
-            <param name="unmapped" value="True"/>
             <output name="mapped_bed" >
                 <assert_contents>
                     <has_text_matching expression="mmu-miR-6898-5p\t11\t21\t2\|2,mmu-miR-6898-5p,11,21,\+,10M39S\t1\t\+" />
@@ -142,7 +141,6 @@
             <param name="ref_type" value="split"/>
             <param name="ref_fasta1" value="ref1.fasta"/>
             <param name="ref_fasta2" value="ref2.fasta"/>
-            <param name="unmapped" value="True"/>
             <output name="mapped_bed" >
                 <assert_contents>
                     <has_text_matching expression="mmu-miR-20a-5p\t0\t23\t3\|2,mmu-miR-20a-5p,0,23,\+,5S23M27S\t1\t\+" />
@@ -167,7 +165,7 @@
 **Output**
 
 * BED file containing the alignments
-* Optional unmapped FASTA file
+* unmapped FASTA file (only for aligner BWA-MEM)
 
     </help>
     <expand macro="citations" />