Mercurial > repos > matthias > stacks2_denovomap
diff macros_process.xml @ 2:fa593b13402f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
| author | matthias |
|---|---|
| date | Tue, 18 Dec 2018 12:57:35 -0500 |
| parents | |
| children | a70c766ce64f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_process.xml Tue Dec 18 12:57:35 2018 -0500 @@ -0,0 +1,235 @@ +<?xml version="1.0"?> + +<!-- macros and tokens for process_radtags and process_short_reads --> + +<macros> + <!-- fastq input for process_radtags/shortreads--> + <xml name="process_inputs"> + <conditional name="input_type"> + <param name="options_type_selector" type="select" label="Single-end or paired-end reads files"> + <option value="single" selected="True">Single-end files</option> + <option value="paired">Paired-end files</option> + </param> + <when value="single"> + <param name="fqinputs" argument="-f" format="fastqsanger,fastqsanger.gz" multiple="true" type="data" label="singles-end reads infile(s)" help="input files" /> + <param name="barcode_encoding" type="select" label="Barcode location"> + <expand macro="barcode_encoding_single" type="Barcode" /> + </param> + </when> + <when value="paired"> + <param name="fqinputs" type="data_collection" collection_type="list:paired" label="paired-end reads infile(s)" format="fastqsanger,fastqsanger.gz"/> + <param name="barcode_encoding" type="select" label="Barcode location"> + <expand macro="barcode_encoding_pair" type="Barcode" /> + </param> + </when> + </conditional> + <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> + </xml> + <token name="@FASTQ_INPUT_PREPROC@"><![CDATA[ + #for $input in $input_type.fqinputs: + #if $input_type.options_type_selector == "single" + #set $isfq=$input.is_of_type('fastqsanger') + #set $name=$clean_ext($input.element_identifier) + #else: + #set $isfq=$input.forward.is_of_type('fastqsanger') + ## TODO if https://github.com/galaxyproject/galaxy/pull/7031 is + ## backported use element_identifier consistently and fix release in <tool>? + #set $name=$clean_ext($input.name) + #end if + + #if $isfq: + #set $ext = "fastq" + #set inputype = "fastq" + #else + #set $ext = "fastq.gz" + #set inputype = "gzfastq" + #end if + + #if $input_type.options_type_selector == "single" + ln -s '$input' 'stacks_inputs/${name}.${ext}' && + #else: + ## procrad needs _R[12]_ in the file name, so we add an add 0 + ln -s '$input.forward' 'stacks_inputs/${name}_R1_0.${ext}' && + ln -s '$input.reverse' 'stacks_inputs/${name}_R2_0.${ext}' && + #end if + #end for + ]]></token> + <token name="@PROCESS_IOOPTIONS@"><![CDATA[ + -p stacks_inputs/ + #if $input_type.options_type_selector == "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 ${on_string} Demultiplexed reads"> + <filter>input_type['options_type_selector'] == "single"</filter> + <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> + </collection> + <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads"> + <filter>input_type['options_type_selector'] == "paired"</filter> + <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> + </collection> + + <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads"> + <filter>input_type['options_type_selector'] == "paired"</filter> + <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.rem\.(?P<identifier_1>[^.]+)" dir="stacks_outputs/remaining"/> + </collection> + + <!-- note irrespective of -y output is always named fastq and are never zipped --> + <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads"> + <filter>capture is True and input_type['options_type_selector'] == "single"</filter> + <expand macro="discover_faq_output_macro" pattern="(?P<name>.*)" dir="stacks_outputs/discarded"/> + </collection> + <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads"> + <filter>capture is True and input_type['options_type_selector'] == "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" 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 $input_type.options_type_selector == 'paired': + && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done + #end if + ## also remove the gz which is added by procrad (but its uncompressed) + && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.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.options_type_selector == '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>