Mercurial > repos > iuc > kallisto_quant

changeset 5:10c98fab6c5a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 4364e7d61b72e12afb7ef294955b1c1e57f757b0
author iuc
date Fri, 30 Nov 2018 06:26:27 -0500
parents b818b23df1e0
children 60f888039fb2
files kallisto_quant.xml
diffstat 1 files changed, 21 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/kallisto_quant.xml	Sat Dec 09 05:33:38 2017 -0500
+++ b/kallisto_quant.xml	Fri Nov 30 06:26:27 2018 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.3">
+<tool id="kallisto_quant" name="Kallisto quant" version="@VERSION@.4">
     <description>- quantify abundances of RNA-Seq transcripts</description>
     <macros>
         <import>macros.xml</import>
@@ -15,7 +15,7 @@
             #set index_path = $reference_transcriptome.index.fields.path
         #end if
         kallisto quant -i '$index_path'
-            $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $pseudobam
+            $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion $lib_type $pseudobam
             #if $pseudobam:
                 -o .
             #else:
@@ -77,6 +77,11 @@
         <param name="bootstrap_samples" argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="default: 0" />
         <param argument="--seed" type="integer" value="42" label="Seed for the bootstrap sampling" help="default: 42" />
         <param argument="--fusion" type="boolean" truevalue="--fusion" falsevalue="" label="Search for fusions" help="for Pizzly" />
+        <param name="lib_type" type="select" label="Library strandness information">
+            <option value="">Unstranded</option>
+            <option value="--fr-stranded">Strand specific reads, first read forward</option>
+            <option value="--rf-stranded">Strand specific reads, first read reverse</option>
+        </param>
         <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
     </inputs>
     <outputs>
@@ -103,6 +108,20 @@
             <param name="reference_transcriptome_source" value="history" />
             <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
             <param name="single_paired_selector" value="paired" />
+            <param name="collection_selector" value="datasets" />
+            <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
+            <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
+            <param name="lib_type" value="--fr-stranded"/>
+            <output name="abundance_tab" >
+                <assert_contents>
+                    <has_text_matching expression="chrM\t16299\t15804.2\t37\t1e\+06" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="reference_transcriptome_source" value="history" />
+            <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
+            <param name="single_paired_selector" value="paired" />
             <param name="collection_selector" value="collection" />
             <param name="reads">
                 <collection type="paired">