Mercurial > repos > trinity_ctat > ctat_abundance_estimation_to_matrix
changeset 6:390cd602c1c1 draft default tip
New ctat_star_fusion.xml to use new bioconda recipe.
author | trinity_ctat |
---|---|
date | Wed, 04 Jul 2018 10:52:38 -0400 |
parents | bf1c59687597 |
children | |
files | ctat_abundance_estimation_to_matrix.xml |
diffstat | 1 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/ctat_abundance_estimation_to_matrix.xml Thu Jun 28 22:44:55 2018 -0400 +++ b/ctat_abundance_estimation_to_matrix.xml Wed Jul 04 10:52:38 2018 -0400 @@ -13,9 +13,9 @@ <command detect_errors="exit_code"> <![CDATA[ python $__tool_directory__/ctat_abundance_estimation_to_matrix.py - #for $q in $RSEM_samples - ${q.file} "${q.column_label}" - #end for +#for $q in $RSEM_samples +${q.file} "${q.column_label}" +#end for ]]> </command> @@ -30,9 +30,9 @@ <outputs> <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.isoform.counts.matrix"/> <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="RSEM.isoform.TMM.EXPR.matrix"/> - </outputs> +</outputs> <tests> - <test> +<test> <repeat name="RSEM_samples"> <param name="file" value="Sp_ds.RSEM.genes.results" /> <param name="column_label" value="Sp_ds" /> @@ -42,7 +42,7 @@ <param name="column_label" value="Sp_hs" /> </repeat> - <output name="counts_matrix" > + <output name="counts_matrix" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="	Sp_ds	Sp_hs" /> @@ -50,7 +50,7 @@ <has_line_matching expression="TRINITY_DN.+" /> </assert_contents> </output> - <output name="tmm_expr_matrix" > + <output name="tmm_expr_matrix" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="	Sp_ds	Sp_hs" /> @@ -60,7 +60,7 @@ </output> </test> <!-- The following test has not been tested to see if it works. - <test> +<test> <repeat name="RSEM_samples"> <param name="file" value="Sp_ds.RSEM.isoforms.results" /> <param name="column_label" value="Sp_ds" /> @@ -70,12 +70,12 @@ <param name="column_label" value="Sp_hs" /> </repeat> - <output name="counts_matrix" > + <output name="counts_matrix" > <assert_contents> <has_line_matching expression=".+" /> </assert_contents> </output> - <output name="tmm_expr_matrix" > + <output name="tmm_expr_matrix" > <assert_contents> <has_line_matching expression=".+" /> </assert_contents>