Mercurial > repos > iuc > colibread_kissplice
diff macros.xml @ 1:d5b4404c4788 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author | iuc |
---|---|
date | Fri, 24 Nov 2017 12:48:06 -0500 |
parents | 4acdd256cc12 |
children | ccc77612cbb9 |
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--- a/macros.xml Fri Oct 20 03:14:17 2017 -0400 +++ b/macros.xml Fri Nov 24 12:48:06 2017 -0500 @@ -1,18 +1,27 @@ <macros> + <xml name="discosnp_requirements"> + <requirements> + <requirement type="package" version="2.3.0">discosnp</requirement> + </requirements> + </xml> + + <token name="@DISCOSNP_VERSION@">2.3.0</token> + <token name="@discosnp_single_reads@"><![CDATA[ #for $input in $input_type_options.list_reads - #set $filename = str($input) + "." + $input.ext + #set $filename = os.path.basename(str($input)) + "." + $input.ext ln -sf '${input}' '${filename}' && echo '${filename}' >> input.lst && #end for ]]></token> + <token name="@discosnp_paired_reads@"><![CDATA[ #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) - #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext + #set $filenameFWD = os.path.basename(str($paired.forward)) + "." + $paired.forward.ext ln -sf '${paired.forward}' '${filenameFWD}' && - #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext + #set $filenameREV = os.path.basename(str($paired.reverse)) + "." + $paired.reverse.ext ln -sf '${paired.reverse}' '${filenameREV}' && echo '${filenameFWD}' > "paired_${i}.lst" && @@ -21,22 +30,121 @@ #end for ]]></token> + + <xml name="discosnp_inputs"> + <conditional name="input_type_options"> + <param name="input_type" type="select" label="Input options"> + <option value="single">Single end reads</option> + <option value="paired">Paired end reads</option> + <option value="mix">Both single and paired reads</option> + </param> + <when value="single"> + <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> + </when> + <when value="paired"> + <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files" /> + </when> + <when value="mix"> + <param name='list_reads' argument="-r" format="fasta,fastq" type="data" multiple="true" label="Single read files" /> + <param name='list_paired_reads' argument="-r" format="fasta,fastq" type="data_collection" collection_type="list:paired" multiple='true' label="List of paired read files"/> + </when> + </conditional> + </xml> + + <xml name="discosnp_options"> + <param argument="-D" type="integer" label="Deletion size" value="0" help="If different of 0, discoSnp will search for deletions of size from 1 to D included"/> + <param argument="-P" type="integer" label="Maximum SNPs per bubble" value="1" help="discoSnp will search up to P SNPs in a unique bubble"/> + <param name="low_complexity" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Remove low complexity bubbles" /> + <param argument="-k" type="integer" label="Size of kmers" value="31" /> + + <conditional name="coverage_options_type" > + <param name="coverage_options" type="select" label="Coverage option"> + <option value="auto"></option> + <option value="custom"></option> + </param> + <when value="auto" /> + <when value="custom"> + <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/> + </when> + </conditional> + + <param argument="-C" type="integer" label="Maximal coverage per read set" value="2147483647" help="default value = 2^31-1" /> + <param argument="-d" type="integer" label="Max number of errors per read" value="1" help="Max number of errors per read" /> + + </xml> + + <token name="@discosnp_inputs@"><![CDATA[ + -r input.lst + -b ${b} + -D ${D} + -P ${P} + ${low_complexity} + -k ${k} + + #if str($coverage_options_type.coverage_options) == 'auto' + -c auto + #else + -c '${coverage_options_type.c}' + #end if + -C ${C} + -d ${d} + ]]></token> + <token name="@lordec_inputs@"><![CDATA[ -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }" -i '${program_type_choice.i}' -k ${program_type_choice.k} -s ${program_type_choice.s} ]]></token> + <xml name="lordec_inputs"> <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> </xml> + + <token name="@discosnp_help@"><![CDATA[ +------- + +.. class:: warningmark + +**Input parameters** + +-Sequences files in fasta or fastq each allele will be counted in each file individually + +-Use collections: data list and/or data list paired + +-Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF + +------- + +.. class:: warningmark + +**Ouput parameters** + +-VCF file with coordinates on the higher branch sequences or on a reference genome if provided + +-Fasta file with sequence extensions around the SNP. + + +------- + +**Web site** + +https://colibread.inria.fr/software/discosnp/ + + ]]></token> + <xml name="citations"> <citations> <yield/> <citation type="doi">10.1186/s13742-015-0105-2</citation> </citations> </xml> + + <xml name="discosnp_citation"> + <citation type="doi">10.1101/209965</citation> + </xml> + </macros>