Mercurial > repos > iuc > hisat2
diff hisat2.xml @ 7:5ba8e317529a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
author | iuc |
---|---|
date | Sat, 21 Jan 2017 15:42:34 -0500 |
parents | 5f4da9ec47c7 |
children | 4d0a3173cde0 |
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--- a/hisat2.xml Wed Nov 09 05:57:35 2016 -0500 +++ b/hisat2.xml Sat Jan 21 15:42:34 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hisat2" name="HISAT" version="2.0.3.1"> +<tool id="hisat2" name="HISAT2" version="2.0.3.2"> <description>A fast and sensitive alignment program</description> <macros> <import>hisat2_macros.xml</import> @@ -38,6 +38,12 @@ @paired_end_options@ #else: -U "${input_format.paired.reads}" + #if str( $input_format.paired.unaligned_file ) == "true": + --un '$output_unaligned_reads_l' + #end if + #if str( $input_format.paired.aligned_file ) == "true": + --al '$output_aligned_reads_l' + #end if #end if #if $input_format.input_format_selector == 'fasta': -f @@ -84,6 +90,22 @@ ${paired_options.dovetail} ${paired_options.contain} ${paired_options.overlap} #end if | samtools sort - -@ \${GALAXY_SLOTS:-2} -l 6 -o hsbam > "${output_alignments}" + + ## Rename any output fastq files + #if str($input_format.paired.paired_selector) == 'paired' or str($input_format.paired.paired_selector) == 'paired_collection': + #if $output_unaligned_reads_l and $output_unaligned_reads_r: + #set left = str($output_unaligned_reads_l).replace(".dat", ".1.dat") + #set right = str($output_unaligned_reads_l).replace(".dat", ".2.dat") + && mv '${left}' '${output_unaligned_reads_l}' + && mv '${right}' '${output_unaligned_reads_r}' + #end if + #if $output_aligned_reads_l and $output_aligned_reads_r: + #set left = str($output_aligned_reads_l).replace(".dat", ".1.dat") + #set right = str($output_aligned_reads_l).replace(".dat", ".2.dat") + && mv '${left}' '${output_aligned_reads_l}' + && mv '${right}' '${output_aligned_reads_r}' + #end if + #end if ]]> </command> <inputs> @@ -243,6 +265,84 @@ </conditional> </actions> </data> + <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > + <filter>input_format['paired']['unaligned_file'] is True</filter> + <actions> + <conditional name="input_format.paired.paired_selector"> + <when value="single"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)" > + <filter>input_format['paired']['unaligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> + <actions> + <conditional name="input_format.paired.paired_selector"> + <when value="paired"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads${' (L)' if str($input_format.paired.paired_selector) != 'single' else ''}" > + <filter>input_format['paired']['aligned_file'] is True</filter> + <actions> + <conditional name="input_format.paired.paired_selector"> + <when value="single"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="ext" /> + </action> + </when> + <when value="paired"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads_f" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)" > + <filter>input_format['paired']['aligned_file'] is True and input_format['paired']['paired_selector'] != 'single'</filter> + <actions> + <conditional name="input_format.paired.paired_selector"> + <when value="paired"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads_r" param_attribute="ext" /> + </action> + </when> + <when value="paired_collection"> + <action type="format"> + <option type="from_param" name="input_format.paired.reads" param_attribute="forward.ext" /> + </action> + </when> + </conditional> + </actions> + </data> </outputs> <tests> <test> @@ -281,6 +381,35 @@ <param name="no_discordant" value="True" /> <output name="output_alignments" ftype="bam" file="hisat_output_3.bam" lines_diff="2" /> </test> + <test><!-- testing unaligned output (single dataset) --> + <param name="input_format_selector" value="fasta" /> + <param name="paired_selector" value="single" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="unaligned_file" value="true" /> + <param name="aligned_file" value="true" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="reads" value="test_unaligned_reads.fasta" ftype="fasta" /> + + <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> + </test> + + <test> + <param name="input_format_selector" value="fasta" /> + <param name="paired_selector" value="paired" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="unaligned_file" value="true" /> + <param name="aligned_file" value="true" /> + <param name="reference_genome_source" value="history" /> + <param name="history_item" value="phiX.fa" ftype="fasta" /> + <param name="reads_f" value="test_unaligned_reads.fasta" ftype="fasta" /> + <param name="reads_r" value="test_unaligned_reads.fasta" ftype="fasta" /> + + <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> + <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> + </test> </tests> <help> <![CDATA[