# HG changeset patch
# User iuc
# Date 1569503484 14400
# Node ID 5ae5c312d718bd4ec5fa54af51d120cc5ca3b06d
# Parent  1c75aa5de15e194dad02c902754d307db4aa167f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f84c314bc721b5b0c7be10eaf287b1830caca241"

diff -r 1c75aa5de15e -r 5ae5c312d718 kallisto_pseudo.xml
--- a/kallisto_pseudo.xml	Sat Dec 09 05:34:01 2017 -0500
+++ b/kallisto_pseudo.xml	Thu Sep 26 09:11:24 2019 -0400
@@ -15,13 +15,8 @@
             #set index_path = $reference_transcriptome.index.fields.path
         #end if
         kallisto pseudo -i '$index_path'
-            #if $pseudobam:
-                $pseudobam -o .
-            #else:
-                --threads \${GALAXY_SLOTS:-1}
-                -o .
-            #end if
-
+            --threads \${GALAXY_SLOTS:-1}
+            -o .
 
             #if str($single_paired.single_paired_selector) == 'single':
                 --single --fragment-length $single_paired.fragment_length
@@ -39,13 +34,10 @@
                     #end if
                 #end if
             #end if
-            #if $pseudobam:
-                | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
-            #end if
             && if [ -f run_info.json ] ; then cat run_info.json ; fi &&
             mkdir outputs &&
             if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
-            if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi &&
+            if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi &&
             if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
             if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
             if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
@@ -106,15 +98,11 @@
                 </conditional>
             </when>
         </conditional>
-        <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
     </inputs>
     <outputs>
         <data format="tabular" name="sample">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" />
         </data>
-        <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)">
-            <filter>pseudobam</filter>
-        </data>
     </outputs>
     <tests>
         <test>
@@ -176,19 +164,6 @@
             <param name="reference_transcriptome_source" value="cached" />
             <param name="single_paired_selector" value="paired" />
             <param name="collection_selector" value="datasets" />
-            <param name="pseudobam" value="true" />
-            <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
-            <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
-            <output name="sample">
-                <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />
-                <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
-            </output>
-            <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
-        </test>
-        <test>
-            <param name="reference_transcriptome_source" value="cached" />
-            <param name="single_paired_selector" value="paired" />
-            <param name="collection_selector" value="datasets" />
             <param name="umi" value="yes" />
             <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
             <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
diff -r 1c75aa5de15e -r 5ae5c312d718 macros.xml
--- a/macros.xml	Sat Dec 09 05:34:01 2017 -0500
+++ b/macros.xml	Thu Sep 26 09:11:24 2019 -0400
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@VERSION@">0.43.1</token>
+    <token name="@VERSION@">0.46.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">kallisto</requirement>
-            <requirement type="package" version="1.5">samtools</requirement>
+            <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 1c75aa5de15e -r 5ae5c312d718 test-data/kallisto_pseudo_out1.tab
--- a/test-data/kallisto_pseudo_out1.tab	Sat Dec 09 05:34:01 2017 -0500
+++ b/test-data/kallisto_pseudo_out1.tab	Thu Sep 26 09:11:24 2019 -0400
@@ -1,2 +1,4 @@
-0	0	100
-0	1	100
+%%MatrixMarket matrix coordinate real general
+2	1	2
+1	1	100
+2	1	100
diff -r 1c75aa5de15e -r 5ae5c312d718 test-data/kallisto_pseudo_out6.tab
--- a/test-data/kallisto_pseudo_out6.tab	Sat Dec 09 05:34:01 2017 -0500
+++ b/test-data/kallisto_pseudo_out6.tab	Thu Sep 26 09:11:24 2019 -0400
@@ -1,2 +1,4 @@
-0	0	18
-0	1	18
+%%MatrixMarket matrix coordinate real general
+2	1	2
+1	1	18
+2	1	18