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annotate concatenate.xml @ 0:7a974f285033 draft

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Initial commit with concatenate and trinity tools. Still testing.
author trinity_ctat
date Mon, 11 Sep 2017 16:40:43 -0400
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children 1e638acde0cf
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1 <tool id="catbash" name="Concatenate datasets">
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2 <description> concatenate datasets from tail to head</description>
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3 <command interpreter="python">
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4 bash_command_executer.py cat
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5 $input1
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6 #for $q in $queries
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7 ${q.input2}
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8 #end for
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9 > $out_file1
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10 </command>
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11 <inputs>
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12 <param name="input1" type="data" label="Concatenate Dataset"/>
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13 <repeat name="queries" title="Dataset">
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14 <param name="input2" type="data" label="Select" />
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15 </repeat>
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16 </inputs>
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17 <outputs>
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18 <data name="out_file1" format="input" metadata_source="input1"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="Sp_ds.left.fq"/>
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23 <param name="input2" value="Sp_hs.left.fq"/>
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24 <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
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25 <assert_contents>
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26 <has_line_matching expression=".+" />
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27 </assert_contents>
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28 </output>
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29 </test>
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30 <test>
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31 <param name="input1" value="Sp_ds.right.fq"/>
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32 <param name="input2" value="Sp_hs.right.fq"/>
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33 <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
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34 <assert_contents>
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35 <has_line_matching expression=".+" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 <!--TODO: if possible, enhance the underlying test code to handle this test
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40 the problem is multiple params with the same name "input2"
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41 <test>
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42 <param name="input1" value="1.bed"/>
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43 <param name="input2" value="2.bed"/>
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44 <param name="input2" value="3.bed"/>
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45 <output name="out_file1" file="cat_wrapper_out2.bed"/>
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46 </test>
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47 -->
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48 </tests>
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49 <help>
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50 .. class:: infomark
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51
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52 Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.
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53
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54 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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55
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56 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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57 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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58 </help>
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59 </tool>