Mercurial > repos > bgruening > 10x_bamtofastq

changeset 1:f71fd828c126 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq commit 60c20816923303efe1185c76f38a5b9a6fb8ce1c
author bgruening
date Thu, 12 May 2022 16:54:20 +0000
parents 110076d77197
children
files 10x_bamtofastq.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/10x_bamtofastq.xml	Tue May 10 12:02:15 2022 +0000
+++ b/10x_bamtofastq.xml	Thu May 12 16:54:20 2022 +0000
@@ -10,7 +10,7 @@
         $produced_from
         $tenx_bam
         outdir &&
-        mv outdir/*/*.fastq.gz outdir
+        cd outdir; for i in */*.fastq.gz;do mv \$i \${i/\//_};done
     ]]></command>
     <inputs>
         <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/>
@@ -51,9 +51,9 @@
         <test>
             <param name="tenx_bam" value="A10.sub.bam"/>
             <output_collection name="fastq_collection" type="list" count="3">
-                <element name="bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
-                <element name="bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
-                <element name="bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
+                <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
+                <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
+                <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
             </output_collection>
         </test>
     </tests>