Mercurial > repos > mvdbeek > repeat_element_identifier

annotate repeat_element_identifier_tool.xml @ 0:f62b463572f0 draft

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planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
author mvdbeek
date Wed, 11 May 2016 13:21:09 -0400
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f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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1 <tool id="repeat_element_identifier" name="repeat_element_identifier" version="0.0.1" hidden="false" >
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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2 <description>Analyze mismatch frequencies in BAM/SAM alignments</description>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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3 <requirements>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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4 </requirements>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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5 <command>>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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6 #for i in $rep
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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7 echo "$i.input_file.element_identifier" > "$output"
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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8 #end for
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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9 </command>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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10 <inputs>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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11 <repeat name="rep" title="input">
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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12 <param name="input_file" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) for which to analyze the mismatches."/>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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13 </repeat>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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14 <outputs>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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15 <data name="output" />
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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16 </outputs>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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17 <tests>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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18 </tests>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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19 <help>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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20 This tool will print the element identifier of files in a repeat section.
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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21 </help>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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22 <citations>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
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23 </citations>
f62b463572f0 planemo upload for repository https://github.com/artbio/tools-artbio commit 3d96056b65a38e7642cfeef4ed274dc76b88472a-dirty
mvdbeek
parents:
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24 </tool>