Mercurial > repos > iuc > rna_starsolo

changeset 12:79b885ce78d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
author iuc
date Tue, 01 Nov 2022 16:57:42 +0000
parents eec9494fdafa
children 9ee34ba73ebf
files rg_rnaStarSolo.xml
diffstat 1 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/rg_rnaStarSolo.xml	Fri Sep 10 16:46:15 2021 +0000
+++ b/rg_rnaStarSolo.xml	Tue Nov 01 16:57:42 2022 +0000
@@ -1,13 +1,13 @@
 <tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT">
     <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
     <xrefs>
         <xref type="bio.tools">star</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="requirements"/>
-    <expand macro="edam"/>
     <expand macro="stdio" >
         <regex match="Segmentation fault" source="both" level="fatal" />
     </expand>
@@ -160,7 +160,7 @@
             <when value="indexed">
                 <conditional name="GTFconditional">
                     <param name="GTFselect" type="select"
-                           label="Reference genome with or without an annotation"
+                           label="Reference genome with annotation"
                            help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and provide your own splice junction annonations.">
                         <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
                         <option value="with-gtf">use genome reference with builtin gene-model</option>
@@ -273,9 +273,9 @@
         </conditional>
         <section name="solo" title="Advanced Settings" expanded="true">
             <param argument="--soloStrand" type="select" label="Strandedness of Library" help="Unstranded has no strand information, Forward has the read strand the same as the original RNA molecule, Reverse has the read strand opposite to the original RNA molecule">
-                <option value="Unstranded" />
-                <option value="Forward" selected="true" />
-                <option value="Reverse" />
+                <option value="Unstranded" >No strand information</option>
+                <option value="Forward" selected="true" >Read strand same as the original RNA molecule</option>
+                <option value="Reverse" >Read strand opposite to the original RNA molecule</option>
             </param>
             <param argument="--soloFeatures" type="select" label="Collect UMI counts for these genomic features" >
                 <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option>