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1 <tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="1.0.0">
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2
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3 <description>Join RSEM estimates from multiple samples into a single matrix</description>
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package">trinity</requirement>
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7 </requirements>
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8 <command interpreter="python">
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9
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10 abundance_estimation_to_matrix_wrapper.py
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11 #for $q in $RSEM_samples
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12 ${q.file} "${q.column_label}"
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13 #end for
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14
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15 </command>
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16 <inputs>
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17
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18 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
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3
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19 <param name="file" label="Add file" type="data" />
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2
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20 <param name="column_label" label="column label" type="text" />
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21 </repeat>
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22
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23 </inputs>
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24 <outputs>
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3
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25 <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
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26 <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <repeat name="RSEM_samples">
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31 <param name="file" value="Sp_ds.RSEM.genes.results" />
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32 <param name="column_label" value="Sp_ds" />
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33 </repeat>
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34 <repeat name="RSEM_samples">
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35 <param name="file" value="Sp_hs.RSEM.genes.results" />
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36 <param name="column_label" value="Sp_hs" />
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37 </repeat>
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38
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39 <output name="counts_matrix" >
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40 <assert_contents>
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41 <has_line_matching expression=".+" />
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42 <has_line line="	Sp_ds	Sp_hs" />
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43 <has_n_columns n="3" />
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44 <has_line_matching expression="TRINITY_DN.+" />
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45 </assert_contents>
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46 </output>
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47 <output name="tmm_expr_matrix" >
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48 <assert_contents>
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49 <has_line_matching expression=".+" />
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50 <has_line line="	Sp_ds	Sp_hs" />
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51 <has_n_columns n="3" />
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52 <has_line_matching expression="TRINITY_DN.+" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 <!-- The following test has not been tested to see if it works.
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57 <test>
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58 <repeat name="RSEM_samples">
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59 <param name="file" value="Sp_ds.RSEM.isoforms.results" />
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60 <param name="column_label" value="Sp_ds" />
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61 </repeat>
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62 <repeat name="RSEM_samples">
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63 <param name="file" value="Sp_hs.RSEM.isoforms.results" />
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64 <param name="column_label" value="Sp_hs" />
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65 </repeat>
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66
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67 <output name="counts_matrix" >
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68 <assert_contents>
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69 <has_line_matching expression=".+" />
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70 </assert_contents>
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71 </output>
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72 <output name="tmm_expr_matrix" >
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73 <assert_contents>
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74 <has_line_matching expression=".+" />
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75 </assert_contents>
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76 </output>
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77 </test>
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78 -->
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79 </tests>
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80 <help>
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81 .. class:: infomark
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82
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83 This step will join the RSEM-computed gene or isoform fragment counts into a matrix file, which will be used to run edgeR and identify differentially expressed transcripts in next few steps. Execution of this will generate a counts matrix file with a name 'abundance_estimation_to_matrix: counts_matrix'.
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84
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85 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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86
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87 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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88 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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89 </help>
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90 </tool>
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