Mercurial > repos > iuc > dexseq

diff dexseq_count.xml @ 18:ffa256d657b2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
author iuc
date Fri, 31 Jan 2025 18:00:29 +0000
parents d104044e4257
children
line wrap: on
line diff
--- a/dexseq_count.xml	Tue Apr 04 08:25:36 2023 +0000
+++ b/dexseq_count.xml	Fri Jan 31 18:00:29 2025 +0000
@@ -16,18 +16,20 @@
     <command><![CDATA[
 #if $mode.mode_select == "prepare":
     dexseq_prepare_annotation.py
-        -r $mode.aggregate
-        '$mode.gtffile'
+        -r '${mode.aggregate}'
+        '${mode.gtffile}'
         '$flattened_gtf_out'
 #elif $mode.mode_select == "count":
+    ln -s -f '${mode.bamfile}' 'input.bam' &&
+    ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' &&
     dexseq_count.py
         --format bam
-        --paired $mode.paired
-        --stranded $mode.stranded
-        --minaqual $mode.qual
-        --order $mode.order
-        $mode.flattened_gtf_in
-        '$mode.bamfile'
+        --paired '${mode.paired}'
+        --stranded '${mode.stranded}'
+        --minaqual '${mode.qual}'
+        --order '${mode.order}'
+        '${mode.flattened_gtf_in}'
+        'input.bam'
         '$counts_file'
     &&
     sed -i 's/\"//g' '$counts_file'
@@ -73,14 +75,14 @@
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="prepare" />
             <param name="gtffile" ftype="gff" value="original.gtf"/>
             <param name="aggregate" value="True"/>
             <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
         </test>
         <!-- Ensure count mode works -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="mode_select" value="count" />
             <param name="bamfile" ftype="bam" value="in.bam" />
             <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>