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1 <tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
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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>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
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6 <!--<version_command></version_command>-->
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7 <command interpreter="python">makeTagDirectory.py ${tagDir.files_path}
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8 #for $alignF in $alignmentFiles
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9 $alignF.file -f $alignF.file.ext
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10 #end for
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11 -o $tagDir
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12 2> $out_log || echo "Error running homer_makeTagDirectory." >&2
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13
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14 </command>
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15 <inputs>
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16 <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
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17 <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
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18 <sanitizer>
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19 <valid initial="string.printable">
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20 <remove value="'"/>
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21 <remove value="/"/>
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22 </valid>
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23 <mapping initial="none">
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24 <add source="'" target="__sq__"/>
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25 </mapping>
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26 </sanitizer>
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27 </param>
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28 <repeat name="alignmentFiles" title="Alignment Files">
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29 <param name="file" label="Add file" type="data" format="sam,bed" />
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30 </repeat>
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31 </inputs>
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32 <outputs>
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33 <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
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34 <data format="html" name="tagDir" label="${title} tag directory" />
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35 <data format="txt" name="out_log" label="${title}.log" />
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36 <!--<data format="html" name="html_outfile" label="index" />-->
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37 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
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38 </outputs>
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39
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40
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41 <tests>
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42 <!--<test>-->
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43 <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
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44 <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
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45 <!--</test>-->
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46 </tests>
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47
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48 <help>
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49
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50 .. class:: infomark
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51
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52 **Homer makeTagDirectory**
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53
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54 For more options, look under: "Command line options"
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55
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56 http://biowhat.ucsd.edu/homer/ngs/tagDir.html
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57
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58
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59 </help>
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60 </tool>
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61
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