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1 <tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 experimental_design/experimental_design.sh
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5 #for $i, $f in enumerate($patients)
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6 "$f.id"
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7 #for $j, $g in enumerate($f.samples)
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8 ${g.sample}
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9 #end for
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10 #end for
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11 $out_file
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12 </command>
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13 <inputs>
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14 <repeat name="patients" title="Patient" min="1" default="1">
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15 <repeat name="samples" title="Sample" min="1" default="1">
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16 <param name="sample" format="tabular" type="data" label="Sample to Process" />
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17 </repeat>
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18 <param name="id" type="text" label="ID" />
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19 </repeat>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="out_file"/>
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23 </outputs>
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24 <help>
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25 Takes the ARGalaxy proprietary format and merges several samples and/or patients together.
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26 </help>
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27 <citations>
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28 <!-- Example of annotating a citation using a DOI. -->
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29 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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30
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31 <!-- Example of annotating a citation using a BibTex entry. -->
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32 <citation type="bibtex">@ARTICLE{Kim07aninterior-point,
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33 author = {Seung-jean Kim and Kwangmoo Koh and Michael Lustig and Stephen Boyd and Dimitry Gorinevsky},
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34 title = {An interior-point method for large-scale l1-regularized logistic regression},
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35 journal = {Journal of Machine Learning Research},
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36 year = {2007},
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37 volume = {8},
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38 pages = {1519-1555}
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39 }</citation>
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40 </citations>
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41 <tests>
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42 <test>
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43 <param name="input" value="1.bed"/>
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44 <param name="column" value="1"/>
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45 <param name="order" value="ASC"/>
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46 <param name="style" value="num"/>
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47 <output name="out_file1" file="sort1_num.bed"/>
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48 </test>
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49 <test>
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50 <param name="input" value="7.bed"/>
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51 <param name="column" value="1"/>
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52 <param name="order" value="ASC"/>
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53 <param name="style" value="alpha"/>
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54 <output name="out_file1" file="sort1_alpha.bed"/>
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55 </test>
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56 </tests>
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57 </tool>
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