diff align_and_estimate_abundance.xml @ 18:00719b8004c9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"

--- a/align_and_estimate_abundance.xml	Fri Sep 10 22:42:30 2021 +0000
+++ b/align_and_estimate_abundance.xml	Sat Nov 27 10:13:50 2021 +0000
@@ -1,9 +1,9 @@
 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1">
     <description>on a de novo assembly of RNA-Seq data</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <requirement type="package" version="1.3.2">rsem</requirement>
         <requirement type="package" version="0.46.0">kallisto</requirement>
@@ -190,11 +190,11 @@
             <param name="left_input" value="reads.left.fq.gz"/>
             <param name="right_input" value="reads.right.fq.gz"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
-            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie"/>
             <param name="has_gene_map" value="yes"/>
+            <param name="gene_trans_map" value="raw/Trinity.map" />
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -213,11 +213,11 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
-            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="RSEM"/>
             <param name="aln_method" value="bowtie2"/>
             <param name="has_gene_map" value="yes"/>
+            <param name="gene_trans_map" value="raw/Trinity.map" />
             <output name="isoforms_counts_rsem">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
@@ -236,11 +236,11 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
-            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="salmon"/>
             <param name="aln_method" value="bowtie"/>
             <param name="has_gene_map" value="yes"/>
+            <param name="gene_trans_map" value="raw/Trinity.map" />
             <output name="isoforms_counts_salmon">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN2_c3_g1_i1&#009;.*" />
@@ -259,10 +259,10 @@
             <param name="left_input" value="reads.left.fq"/>
             <param name="right_input" value="reads.right.fq"/>
             <param name="transcripts" value="raw/Trinity.fasta"/>
-            <param name="gene_to_trans" value="raw/Trinity.map" />
             <param name="library_type" value="RF"/>
             <param name="est_method" value="kallisto"/>
             <param name="has_gene_map" value="yes"/>
+            <param name="gene_trans_map" value="raw/Trinity.map" />
             <output name="isoforms_counts_kallisto">
                 <assert_contents>
                     <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />