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1 <tool id="ctat_abundance_estimation_to_matrix" name="ctat_abundance_estimation_to_matrix" version="1.0.0" profile="17.05">
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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">subprocess32</requirement>
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7 <requirement type="package">bzip2</requirement>
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8 <requirement type="package" version="1.3.0">rsem</requirement>
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9 <requirement type="package" version="3">bioconductor-edger</requirement>
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10 <requirement type="package" version="2">bioconductor-qvalue</requirement>
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11 <requirement type="package" version="2.6.6">trinity</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 python $__tool_directory__/ctat_abundance_estimation_to_matrix.py
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16 #for $q in $RSEM_samples
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17 ${q.file} "${q.column_label}"
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18 #end for
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19 ]]>
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20
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21 </command>
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22 <inputs>
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23
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24 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
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25 <param name="file" label="Add file" type="data" format="txt"/>
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26 <param name="column_label" label="column label" type="text" />
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27 </repeat>
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28
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.isoform.counts.matrix"/>
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32 <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="RSEM.isoform.TMM.EXPR.matrix"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <repeat name="RSEM_samples">
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37 <param name="file" value="Sp_ds.RSEM.genes.results" />
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38 <param name="column_label" value="Sp_ds" />
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39 </repeat>
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40 <repeat name="RSEM_samples">
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41 <param name="file" value="Sp_hs.RSEM.genes.results" />
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42 <param name="column_label" value="Sp_hs" />
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43 </repeat>
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44
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45 <output name="counts_matrix" >
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46 <assert_contents>
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47 <has_line_matching expression=".+" />
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48 <has_line line="	Sp_ds	Sp_hs" />
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49 <has_n_columns n="3" />
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50 <has_line_matching expression="TRINITY_DN.+" />
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51 </assert_contents>
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52 </output>
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53 <output name="tmm_expr_matrix" >
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54 <assert_contents>
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55 <has_line_matching expression=".+" />
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56 <has_line line="	Sp_ds	Sp_hs" />
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57 <has_n_columns n="3" />
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58 <has_line_matching expression="TRINITY_DN.+" />
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <!-- The following test has not been tested to see if it works.
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63 <test>
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64 <repeat name="RSEM_samples">
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65 <param name="file" value="Sp_ds.RSEM.isoforms.results" />
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66 <param name="column_label" value="Sp_ds" />
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67 </repeat>
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68 <repeat name="RSEM_samples">
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69 <param name="file" value="Sp_hs.RSEM.isoforms.results" />
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70 <param name="column_label" value="Sp_hs" />
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71 </repeat>
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72
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73 <output name="counts_matrix" >
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74 <assert_contents>
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75 <has_line_matching expression=".+" />
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76 </assert_contents>
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77 </output>
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78 <output name="tmm_expr_matrix" >
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79 <assert_contents>
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80 <has_line_matching expression=".+" />
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81 </assert_contents>
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82 </output>
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83 </test>
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84 -->
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85 </tests>
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86 <help>
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87 .. class:: infomark
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88
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89 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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90
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91 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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92
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93 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
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94 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
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95 </help>
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96
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97 <citations>
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98 <citation type="doi">10.1038/nbt.1883</citation>
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99 </citations>
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100
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101 </tool>
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