Mercurial > repos > bgruening > sailfish
changeset 1:06646e81c543 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sailfish commit 326fbf6e8070a792e3bda3256e5465c2d5b1eb71
| author | bgruening |
|---|---|
| date | Tue, 10 Nov 2015 20:19:23 -0500 |
| parents | 3b4ed0e473dc |
| children | 20eab032389f |
| files | sailfish.xml |
| diffstat | 1 files changed, 26 insertions(+), 11 deletions(-) [+] |
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--- a/sailfish.xml Fri Oct 16 15:09:03 2015 -0400 +++ b/sailfish.xml Tue Nov 10 20:19:23 2015 -0500 @@ -6,9 +6,9 @@ <macros> <xml name="strandedness"> <param name="strandedness" type="select" label="Specify the strandedness of the reads"> - <option value="U" selected="True">Not stranded</option> - <option value="SF">read 1 (or single-end read) comes from the forward strand</option> - <option value="SR">read 1 (or single-end read) comes from the reverse strand</option> + <option value="U" selected="True">Not stranded (U)</option> + <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option> + <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option> </param> </xml> </macros> @@ -17,6 +17,7 @@ <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> + <regex match="Exception :" /> </stdio> <version_command>sailfish -version</version_command> <command> @@ -36,10 +37,24 @@ && #if $single_or_paired.single_or_paired_opts == 'single': - ln -s $single_or_paired.input_singles ./single.$single_or_paired.input_singles.ext && + + #if $single_or_paired.input_singles.ext == 'fasta': + #set $ext = 'fasta' + #else: + #set $ext = 'fastq' + #end if + + ln -s $single_or_paired.input_singles ./single.$ext && #else: - ln -s $single_or_paired.input_mate1 ./mate1.$single_or_paired.input_mate1.ext && - ln -s $single_or_paired.input_mate2 ./mate2.$single_or_paired.input_mate2.ext && + + #if $single_or_paired.input_mate1.ext == 'fasta': + #set $ext = 'fasta' + #else: + #set $ext = 'fastq' + #end if + + ln -s $single_or_paired.input_mate1 ./mate1.$ext && + ln -s $single_or_paired.input_mate2 ./mate2.$ext && #end if @@ -50,11 +65,11 @@ sailfish quant --index $index_path #if $single_or_paired.single_or_paired_opts == 'single': - --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" - --unmated_reads ./single.$single_or_paired.input_singles.ext + --libType ${single_or_paired.strandedness} + --unmatedReads ./single.$ext #else: - --mates1 ./mate1.$single_or_paired.input_mate1.ext - --mates2 ./mate2.$single_or_paired.input_mate2.ext + --mates1 ./mate1.$ext + --mates2 ./mate2.$ext --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if --output ./ @@ -173,7 +188,7 @@ <outputs> <data name="output_quant" format="tabular" from_work_dir="quant.sf" label="${tool.name} on ${on_string} (Quantification)" /> <data name="output_bias_corrected_quant" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)"> - <filter>bias_correct == '--biasCorrect'</filter> + <filter>biasCorrect is True</filter> </data> <data name="output_gene_quant" format="tabular" from_work_dir="quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)"> <filter>geneMap is True</filter>