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comparison 10x_bamtofastq.xml @ 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
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0:110076d77197 1:f71fd828c126
8 --locus $convert.locus 8 --locus $convert.locus
9 #end if 9 #end if
10 $produced_from 10 $produced_from
11 $tenx_bam 11 $tenx_bam
12 outdir && 12 outdir &&
13 mv outdir/*/*.fastq.gz outdir 13 cd outdir; for i in */*.fastq.gz;do mv \$i \${i/\//_};done
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/> 16 <param format="bam" name="tenx_bam" type="data" label="10X Genomics BAM file to convert to FASTQ"/>
17 <conditional name="convert"> 17 <conditional name="convert">
18 <param name="reads" type="select" label="Read pairs to convert?"> 18 <param name="reads" type="select" label="Read pairs to convert?">
49 49
50 <tests> 50 <tests>
51 <test> 51 <test>
52 <param name="tenx_bam" value="A10.sub.bam"/> 52 <param name="tenx_bam" value="A10.sub.bam"/>
53 <output_collection name="fastq_collection" type="list" count="3"> 53 <output_collection name="fastq_collection" type="list" count="3">
54 <element name="bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/> 54 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_I1_001" file="bamtofastq_S1_L007_I1_001.fastq.gz"/>
55 <element name="bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/> 55 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R1_001" file="bamtofastq_S1_L007_R1_001.fastq.gz"/>
56 <element name="bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/> 56 <element name="A10_MissingLibrary_1_CB54YACXX_bamtofastq_S1_L007_R2_001" file="bamtofastq_S1_L007_R2_001.fastq.gz"/>
57 </output_collection> 57 </output_collection>
58 </test> 58 </test>
59 </tests> 59 </tests>
60 <help><![CDATA[ 60 <help><![CDATA[
61 10x Genomics BAM to FASTQ converter 61 10x Genomics BAM to FASTQ converter