Mercurial > repos > bebatut > sortmerna
diff sortmerna.xml @ 16:1a4662c2d6db draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 044a991b45c9135339daf138929887cd8e93a1bf-dirty
| author | bebatut |
|---|---|
| date | Mon, 12 Jun 2017 06:20:50 -0400 |
| parents | baab049d3aff |
| children | 715c75d6d784 |
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--- a/sortmerna.xml Wed Feb 10 04:02:18 2016 -0500 +++ b/sortmerna.xml Mon Jun 12 06:20:50 2017 -0400 @@ -1,7 +1,10 @@ -<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1.0"> +<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.4"> <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="2.0">sortmerna</requirement> + <requirement type="package" version="@VERSION@">sortmerna</requirement> </requirements> <stdio> <regex match="This program builds a Burst trie on an input rRNA database" @@ -35,14 +38,14 @@ ## databases path is not directly accessible, must match by hand with LOC file contents #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value - #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed' + #set $ref += $sep + $databases_type.input_databases.path + '.fasta,' + $databases_type.input_databases.path + '-reindexed' #set $sep = ':' #end for #else: ## databases path is not directly accessible, must match by hand with LOC file contents #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value - #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + #set $ref += $sep + $databases_type.input_databases.path + '.fasta,' + $databases_type.input_databases.path #set $sep = ':' #end for #end if @@ -75,7 +78,9 @@ #if $aligned_sam.aligned_sam_selector == '--sam' $aligned_sam.sq #end if - $aligned_blast + #if $aligned_blast.aligned_blast_selector == '--blast' + --blast "$aligned_blast.aligned_blast_format" + #end if $log @@ -115,8 +120,8 @@ <when value="paired"> <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not"> <option value="">leave the reads split between aligned and rejected files</option> - <option value="--paired-in">output both reads to aligned file (--paired-in)</option> - <option value="--paired-out">output both reads to rejected file (--paired-out)</option> + <option value="--paired_in">output both reads to aligned file (--paired_in)</option> + <option value="--paired_out">output both reads to rejected file (--paired_out)</option> </param> </when> </conditional> @@ -179,14 +184,23 @@ </when> <when value="" /> </conditional> - <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format"> - <option value="--blast 0">pairwise (--blast 0)</option> - <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option> - <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option> - <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option> - <option value="" selected="true">No</option> - </param> - <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file" + <conditional name="aligned_blast"> + <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?"> + <option value="--blast">Yes</option> + <option value="" selected="true">No</option> + </param> + <when value="--blast"> + <param name="aligned_blast_format" type="select" label="BLAST-like format?"> + <option value="0">pairwise (--blast '0')</option> + <option value="1">tabular BLAST -m 8 format (--blast '1')</option> + <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option> + <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option> + <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option> + </param> + </when> + <when value="" /> + </conditional> + <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file" help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)"> </param> <conditional name="report"> @@ -247,9 +261,9 @@ </data> <data format="tabular" name="output_blast" from_work_dir="aligned.blast" label="Alignments on ${on_string} (BLAST)"> - <filter>aligned_blast</filter> + <filter>aligned_blast['aligned_blast_selector']</filter> <change_format> - <when input="aligned_blast" value="--blast 0" format="txt" /> + <when input="aligned_blast.aligned_blast_format" value="0" format="txt" /> </change_format> </data> <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log"> @@ -263,8 +277,20 @@ <param name="strand_search" value="" /> <param name="databases_selector" value="history" /> <param name="database_name" value="ref_small.fasta" /> + <param name="aligned_fastx_selector" value="--fastx" /> <param name="other" value="True" /> + <param name="aligned_sam_selector" value="--sam" /> + <param name="aligned_blast_selector" value="--blast"/> + <param name="aligned_blast_format" value="1 cigar qcov" /> <param name="log" value="" /> + <param name="report_type" value="best" /> + <param name="report_best_type" value="1" /> + <param name="e_value" value="1"/> + <param name="match" value="2"/> + <param name="mismatch" value="-3" /> + <param name="gap_open" value="5"/> + <param name="gap_ext" value="2"/> + <param name="ambiguous_letter" value="-3"/> <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" /> <output name="output_other" file="sortmerna_wrapper_other1.fastq" /> <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" /> @@ -275,8 +301,21 @@ <param name="strand_search" value="" /> <param name="databases_selector" value="history" /> <param name="database_name" value="ref_small.fasta" /> + <param name="aligned_fastx_selector" value="--fastx" /> <param name="other" value="True" /> + <param name="aligned_sam_selector" value="--sam" /> + <param name="aligned_blast" value="" /> <param name="log" value="" /> + <param name="report_type" value="best" /> + <param name="report_best_type" value="1" /> + <param name="report_type" value="best" /> + <param name="report_best_type" value="1" /> + <param name="e_value" value="1"/> + <param name="match" value="2"/> + <param name="mismatch" value="-3" /> + <param name="gap_open" value="5"/> + <param name="gap_ext" value="2"/> + <param name="ambiguous_letter" value="-3"/> <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" /> <output name="output_other" file="sortmerna_wrapper_other2.fasta" /> <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />