Mercurial > repos > trinity_ctat > abundance_estimation_to_matrix
annotate abundance_estimation_to_matrix.xml @ 8:f7a95f936503 draft
Adding EdgeR differential expression.
| author | trinity_ctat |
|---|---|
| date | Fri, 29 Sep 2017 13:44:24 -0400 |
| parents | deed5e162203 |
| children | 4c943e196e8f |
| rev | line source |
|---|---|
| 0 | 1 <tool id="abundance_estimation_to_matrix" name="abundance_estimation_to_matrix" version="1.0.0"> |
| 2 | |
| 3 <description>Join RSEM estimates from multiple samples into a single matrix</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.7">python</requirement> | |
| 6 <requirement type="package">trinity</requirement> | |
| 7 </requirements> | |
| 6 | 8 <command> |
| 9 <![CDATA[ | |
|
7
deed5e162203
Adding __tool_directory__ before the wrapper name.
trinity_ctat
parents:
6
diff
changeset
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10 python $__tool_directory__/abundance_estimation_to_matrix_wrapper.py |
| 0 | 11 #for $q in $RSEM_samples |
| 12 ${q.file} "${q.column_label}" | |
| 13 #end for | |
| 6 | 14 ]]> |
| 0 | 15 |
| 16 </command> | |
| 17 <inputs> | |
| 18 | |
| 19 <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> | |
| 6 | 20 <param name="file" label="Add file" type="data" format="txt"/> |
| 2 | 21 <param name="column_label" label="column label" type="text" /> |
| 0 | 22 </repeat> |
| 23 | |
| 24 </inputs> | |
| 25 <outputs> | |
| 6 | 26 <data format="txt" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/> |
| 27 <data format="txt" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/> | |
| 0 | 28 </outputs> |
| 29 <tests> | |
| 30 <test> | |
| 31 <repeat name="RSEM_samples"> | |
| 32 <param name="file" value="Sp_ds.RSEM.genes.results" /> | |
| 33 <param name="column_label" value="Sp_ds" /> | |
| 34 </repeat> | |
| 35 <repeat name="RSEM_samples"> | |
| 36 <param name="file" value="Sp_hs.RSEM.genes.results" /> | |
| 37 <param name="column_label" value="Sp_hs" /> | |
| 38 </repeat> | |
| 39 | |
| 40 <output name="counts_matrix" > | |
| 41 <assert_contents> | |
| 42 <has_line_matching expression=".+" /> | |
| 43 <has_line line="	Sp_ds	Sp_hs" /> | |
| 44 <has_n_columns n="3" /> | |
| 45 <has_line_matching expression="TRINITY_DN.+" /> | |
| 46 </assert_contents> | |
| 47 </output> | |
| 48 <output name="tmm_expr_matrix" > | |
| 49 <assert_contents> | |
| 50 <has_line_matching expression=".+" /> | |
| 51 <has_line line="	Sp_ds	Sp_hs" /> | |
| 52 <has_n_columns n="3" /> | |
| 53 <has_line_matching expression="TRINITY_DN.+" /> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 </test> | |
| 57 <!-- The following test has not been tested to see if it works. | |
| 58 <test> | |
| 59 <repeat name="RSEM_samples"> | |
| 60 <param name="file" value="Sp_ds.RSEM.isoforms.results" /> | |
| 61 <param name="column_label" value="Sp_ds" /> | |
| 62 </repeat> | |
| 63 <repeat name="RSEM_samples"> | |
| 64 <param name="file" value="Sp_hs.RSEM.isoforms.results" /> | |
| 65 <param name="column_label" value="Sp_hs" /> | |
| 66 </repeat> | |
| 67 | |
| 68 <output name="counts_matrix" > | |
| 69 <assert_contents> | |
| 70 <has_line_matching expression=".+" /> | |
| 71 </assert_contents> | |
| 72 </output> | |
| 73 <output name="tmm_expr_matrix" > | |
| 74 <assert_contents> | |
| 75 <has_line_matching expression=".+" /> | |
| 76 </assert_contents> | |
| 77 </output> | |
| 78 </test> | |
| 79 --> | |
| 80 </tests> | |
| 81 <help> | |
| 82 .. class:: infomark | |
| 83 | |
| 84 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'. | |
| 85 | |
| 86 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_. | |
| 87 | |
| 88 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki | |
| 89 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html | |
| 90 </help> | |
| 4 | 91 |
| 92 <citations> | |
| 93 <citation type="doi">10.1038/nbt.1883</citation> | |
| 94 </citations> | |
| 95 | |
| 0 | 96 </tool> |