Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/galaxy/testArgum.xml @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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| -1:000000000000 | 0:e0f8dcca02ed |
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| 1 <tool id="test_argument" name="test_argu" version="1.0.0"> | |
| 2 <description>To test the arguments from shell.</description> | |
| 3 <command> | |
| 4 ../testArgu.sh $test_out | |
| 5 #for $i in $replicate_groups | |
| 6 #for $j in $i.replicates | |
| 7 $j.bam_alignment:#slurp | |
| 8 #end for | |
| 9 #end for | |
| 10 >> $Log_File </command> | |
| 11 <inputs> | |
| 12 <param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/> | |
| 13 <repeat name="replicate_groups" title="Replicate group" min="2"> | |
| 14 <repeat name="replicates" title="Replicate"> | |
| 15 <param format="fastq" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/> | |
| 16 </repeat> | |
| 17 </repeat> | |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="txt" name="test_out" label="DESeq result"/> | |
| 22 <data format="txt" name="Log_File" label="DESeq result"/> | |
| 23 </outputs> | |
| 24 </tool> |