Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/testArgum.xml @ 4:1fc014126d55

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Uploaded
author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 <tool id="test_argument" name="test_argu" version="1.0.0">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 <description>To test the arguments from shell.</description>
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3 <command>
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4 ../testArgu.sh $test_out
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 #for $i in $replicate_groups
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6 #for $j in $i.replicates
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 $j.bam_alignment:#slurp
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8 #end for
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #end for
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 >> $Log_File </command>
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11 <inputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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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"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 <repeat name="replicate_groups" title="Replicate group" min="2">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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14 <repeat name="replicates" title="Replicate">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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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."/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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16 </repeat>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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17 </repeat>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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18 </inputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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20 <outputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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21 <data format="txt" name="test_out" label="DESeq result"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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22 <data format="txt" name="Log_File" label="DESeq result"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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23 </outputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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24 </tool>