Mercurial > repos > iuc > stacks2_tsv2bam
view macros_process.xml @ 1:8c2617661c49 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author | iuc |
---|---|
date | Mon, 30 Sep 2019 14:20:19 -0400 |
parents | 1b270fc77c81 |
children | bf0e43ab0416 |
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<?xml version="1.0"?> <!-- macros and tokens for process_radtags and process_short_reads --> <macros> <token name="@PROCESS_IOOPTIONS@"><![CDATA[ -p stacks_inputs/ #if $input_type.input_type_select == "paired" --paired #end if -i $inputype -b '$barcode' $input_type.barcode_encoding #if str( $outype ) != "auto" -y $outype #end if -o stacks_outputs ]]></token> <xml name="process_output_types"> <param name="outype" argument="-y" type="select" label="Output format" > <option value="auto" selected="True">Same as input</option> <option value="fastq">fastq</option> <option value="fasta">fasta</option> <option value="gzfastq">gzipped fastq</option> <option value="gzfasta">gzipped fasta</option> </param> </xml> <xml name="discover_faqgz_output_macro" token_pattern="" token_dir=""> <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/> <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" /> <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" /> </xml> <xml name="discover_faq_output_macro" token_pattern="" token_dir=""> <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" /> <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" /> </xml> <xml name="process_outputs"> <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads"> <filter>input_type['input_type_select'] == "single"</filter> <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> </collection> <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads"> <filter>input_type['input_type_select'] == "paired"</filter> <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> </collection> <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads"> <filter>input_type['input_type_select'] == "paired"</filter> <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.rem\.(?P<identifier_1>[^.]+)" dir="stacks_outputs/remaining"/> </collection> <!-- note irrespective of -y output is always named fastq and are never zipped --> <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads"> <filter>capture is True and input_type['input_type_select'] == "single"</filter> <expand macro="discover_faq_output_macro" pattern="(?P<name>.*)" dir="stacks_outputs/discarded"/> </collection> <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads"> <filter>capture is True and input_type['input_type_select'] == "paired"</filter> <expand macro="discover_faq_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs/discarded"/> </collection> </xml> <!-- FASTQ filtering options --> <xml name="process_filter"> <conditional name="filter_cond" > <param name="filter_select" type="select" label="Do quality filtering"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" /> <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" /> <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> </when> <when value="no"> <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> </when> </conditional> <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> </xml> <token name="@PROCESS_FILTER@"><![CDATA[ #if $filter_cond.filter_select == 'yes': -w $filter_cond.sliding -s $filter_cond.score $filter_cond.remove $filter_cond.discard $filter_cond.filter_illumina #else #if str($filter_cond.len_limit) != "": --len_limit $filter_cond.len_limit #end if #end if $capture ]]></token> <token name="@PROCESS_FASTQ_POSTPROC@"><![CDATA[ #if $capture: && mkdir stacks_outputs/discarded/ && mv stacks_outputs/*discards stacks_outputs/discarded/ ## fix the _R[12]_0 that was added for preparing the input #if $input_type.input_type_select == 'paired': && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done #end if ## also remove the gz which is added by procrad (but its uncompressed) && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done ## the discard files are named fastq even if the output is fasta #if str($outype).endswith("fasta"): && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done #else && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done #end if #end if ## prepare paired read output for processing in galaxy #if $input_type.input_type_select == 'paired': && mkdir stacks_outputs/remaining && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done #end if ]]></token> <!-- adapter trimming options --> <xml name="process_adapter"> <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" /> <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" /> <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/> </xml> <token name="@PROCESS_ADAPTER@"><![CDATA[ ## Adapter options #if str($options_advanced.adapter_1) != "": --adapter_1 $options_advanced.adapter_1 #end if #if str($options_advanced.adapter_2) != "": --adapter_2 $options_advanced.adapter_2 #end if #if str($options_advanced.adapter_mm) != "": --adapter_mm $options_advanced.adapter_mm #end if ]]></token> <!-- barcode rescue options --> <xml name="rescue_barcode"> <conditional name="rescue_cond"> <param name="rescue" type="select" argument="-r" label="Rescue mutated barcodes and RAD-Tags?"> <option value="-r">yes</option> <option value="" selected="true">no</option> </param> <when value="-r"> <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/> <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/> </when> <when value=""/> </conditional> </xml> <token name="@RESCUE_BARCODE@"><![CDATA[ #if str($options_advanced.rescue_cond.rescue) != "" $options_advanced.rescue_cond.rescue #if str($options_advanced.rescue_cond.barcode_dist_1) != "": --barcode_dist_1 $options_advanced.rescue_cond.barcode_dist_1 #end if #if str($options_advanced.rescue_cond.barcode_dist_2) != "": --barcode_dist_2 $options_advanced.rescue_cond.barcode_dist_2 #end if #end if ]]></token> <!-- advanced options that are shared --> <xml name="common_advanced"> <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" /> </xml> <token name="@COMMON_ADVANCED@"><![CDATA[ #if str($options_advanced.truncate) -t $options_advanced.truncate #end if $options_advanced.retain_header ]]></token> </macros>