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1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="0.0.8">
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2 <requirements>
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3 <requirement type="package" >homer</requirement>
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4 </requirements>
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5 <description>makeTagDirectory</description>
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6 <version_command>echo "Doh!"</version_command>
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7 <command> makeTagDirectory ${tagDir.extra_files_path}
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8 #for $alignF in $alignmentFiles
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9 $alignF.file -format $alignF.file.ext
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10 #end for
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11 2> $out_log || echo "Error running homer_makeTagDirectory." >&2
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12
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13 </command>
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14 <inputs>
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15 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
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16 <repeat name="alignmentFiles" title="Alignment Files">
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17 <param name="file" label="Add file" type="data" format="sam,bed" />
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18 </repeat>
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19 </inputs>
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20 <outputs>
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21 <data format="homerTagDirectory" name="tagDir" label="${title}" />
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22 <data format="txt" name="out_log" label="${title}.log" />
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23 <!--<data format="html" name="html_outfile" label="index" />-->
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24 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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25 </outputs>
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26
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27
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28 <tests>
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29 <!--<test>-->
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30 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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31 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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32 <!--</test>-->
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33 </tests>
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34
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35 <help>
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36
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37 .. class:: infomark
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38
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39 After the job finishes, save the zip file, unzip and open "index.html"
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40
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41 The actual meme-chip command is displayed under "Command line summary"
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42
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43 Defaults:
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44 http://meme.nbcr.net/meme/doc/meme-chip.html
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45
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46 </help>
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47 </tool>
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48
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