Mercurial > repos > trinity_ctat > concatenate

annotate concatenate.xml @ 7:43cb585e9e1c draft

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Adding some debugging statements.
author trinity_ctat
date Mon, 02 Oct 2017 13:50:31 -0400
parents 61f9bd0bac95
children 323f676857c8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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61f9bd0bac95 Making a different repo, because it was decided to set tool versions to 1.0.0 and that caused some probs getting the right ones.
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1 <tool id="catbash" name="Concatenate datasets" version="1.0.0">
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2 <description> concatenate datasets from tail to head</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 </requirements>
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6
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7 <command>
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8 <![CDATA[
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9 python $__tool_directory__/bash_command_executer.py cat
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10 $input1
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11 #for $q in $queries
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12 ${q.input2}
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13 #end for
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14 > $out_file1
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="input1" type="data" label="Concatenate Dataset"/>
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19 <repeat name="queries" title="Dataset">
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20 <param name="input2" type="data" label="Select" />
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21 </repeat>
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22 </inputs>
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23 <outputs>
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24 <data name="out_file1" format="input" metadata_source="input1"/>
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25 </outputs>
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26
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27 <tests>
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28 <test>
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29 <param name="input1" value="Sp_ds.left.fq"/>
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30 <param name="input2" value="Sp_hs.left.fq"/>
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31 <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
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32 <assert_contents>
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33 <has_line_matching expression=".+" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 <test>
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38 <param name="input1" value="Sp_ds.right.fq"/>
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39 <param name="input2" value="Sp_hs.right.fq"/>
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40 <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
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41 <assert_contents>
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42 <has_line_matching expression=".+" />
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43 </assert_contents>
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44 </output>
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45 </test>
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46 <!--TODO: if possible, enhance the underlying test code to handle this test
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47 the problem is multiple params with the same name "input2"
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48 <test>
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49 <param name="input1" value="1.bed"/>
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50 <param name="input2" value="2.bed"/>
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51 <param name="input2" value="3.bed"/>
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52 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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53 </test>
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54 -->
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55 </tests>
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56 <help>
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57 .. class:: infomark
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58
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59 Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.
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60
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61 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
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62
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63 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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64 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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65 </help>
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66 </tool>