Mercurial > repos > iuc > stacks2_kmerfilter
view stacks_kmerfilter.xml @ 1:38c9f9a680f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author | iuc |
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date | Mon, 30 Sep 2019 14:18:47 -0400 |
parents | b2e3553e1be2 |
children | 8a55d29c8fcf |
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<tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> <description>Identify PCR clones</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="version_cmd"/> <command detect_errors="aggressive"><![CDATA[ @FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs && #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select) $link_command kmer_filter #if $input_type.input_type_select == 'single': -f '$fwd_path' #else -1 '$fwd_path' -2 '$rev_path' #end if ## TODO $options_kmer_char.read_k_freq -i $inputype -o stacks_outputs $capture -y fastq $options_filtering.rare $options_filtering.abundant --k_len $options_filtering.k_len --max_k_freq $options_advanced_filtering.max_k_freq #if str($options_advanced_filtering.min_lim)!="": --min_lim $options_advanced_filtering.min_lim #end if #if str($options_advanced_filtering.max_lim)!="": --max_lim $options_advanced_filtering.max_lim #end if #if str($options_normalization.normalize)!="": --normalize $options_normalization.normalize #end if #if $options_kmer_char.write_k_freq --read_k_freq $kfreq #end if $options_kmer_char.k_dist #if $options_kmer_char.k_dist | sed 's/KmerFrequency/# KmerFrequency/' > $kfreqdist #end if @TEE_APPEND_LOG@ @CAT_LOG_TO_STDERR@ ## move outputs such that Galaxy can find them ## if filtering is on then ...filt...fq is created ## if normalization is on then ...norm...fq is created ## if both are active then both files are created, but only norm is needed #if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="": #if str($options_normalization.normalize)!="": #set infix="norm" #else #set infix="fil" #end if #if $capture: #if $input_type.input_type_select == "single" && mv stacks_outputs/*.discards.fastq '$discarded' #else && mv stacks_outputs/*.1.discards.fastq '$discarded_pair.forward' && mv stacks_outputs/*.2.discards.fastq '$discarded_pair.reverse' #end if #end if #if $input_type.input_type_select == "single" && mv stacks_outputs/*.${infix}.fastq '$clean' #else && mv stacks_outputs/*.1.${infix}.fastq '$clean_pair.forward' && mv stacks_outputs/*.2.${infix}.fastq '$clean_pair.reverse' #end if #end if ]]></command> <inputs> <expand macro="fastq_input_bc"/> <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> <section name="options_filtering" title="Filtering options" expanded="False"> <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" /> <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" /> <param argument="--k_len" type="integer" value="15" label="K-mer size" /> </section> <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False"> <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant" /> <param argument="--min_lim" type="integer" value="" optional="true" label="Number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)." /> <param argument="--max_lim" type="integer" value="" optional="true" label="Number of abundant kmers required to discard a read" help="(default: 80% of the k-mers in a read)" /> </section> <section name="options_normalization" title="Normalization options" expanded="False"> <param argument="--normalize" type="integer" value="" optional="true" label="Normalize read depth according to k-mer coverage" /> </section> <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False"> <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="Write kmers along with their frequency of occurrence and exit" /> <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="Print k-mer frequency distribution and exit" /> </section> <!--<section name="options_advanced_input" title="Advanced input options" expanded="False"> <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="Read a set of kmers along with their frequencies of occurrence instead of reading raw input files" /> </section>--> <expand macro="in_log"/> </inputs> <outputs> <expand macro="out_log"/> <data name="clean" format="fastqsanger" label="${tool.name} on ${on_string}"> <filter>input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter> </data> <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}"> <filter>input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter> </collection> <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads"> <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter> </data> <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads"> <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter> </collection> <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies"> <filter>options_kmer_char['write_k_freq']</filter> </data> <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution"> <filter>options_kmer_char['k_dist']</filter> </data> </outputs> <tests> <!-- default output for filtering --> <test> <conditional name="input_type"> <param name="input_type_select" value="single" /> <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> </conditional> <param name="add_log" value="yes" /> <output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/> <param name="rare" value="--rare"/> <param name="abundant" value="--abundant" /> <param name="k_len" value="16" /> <assert_command> <has_text text="--rare" /> <has_text text="--abundant" /> <has_text text="--k_len 16" /> </assert_command> <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> </test> <test> <conditional name="input_type"> <param name="input_type_select" value="paired" /> <param name="fqinputs"> <collection type="paired"> <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> </collection> </param> </conditional> <param name="capture" value="-D" /> <param name="normalize" value="1" /> <assert_command> <has_text text="--normalize 1" /> </assert_command> <output_collection name="clean_pair" type="paired"> <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> </output_collection> <output_collection name="discarded_pair" type="paired"> <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> </output_collection> </test> <!-- kfreq output --> <test> <conditional name="input_type"> <param name="input_type_select" value="single" /> <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> </conditional> <section name="options_kmer_char"> <param name="write_k_freq" value="--write_k_freq" /> </section> <output name="kfreq" file="kmerfilter/kfreq.tsv"/> </test> <!-- kfreqdist output --> <test> <conditional name="input_type"> <param name="input_type_select" value="single" /> <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> </conditional> <section name="options_kmer_char"> <param name="k_dist" value="--k_dist" /> </section> <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/> </test> </tests> <help> <![CDATA[ .. class:: infomark Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data. @STACKS_INFOS@ ]]> </help> <expand macro="citation" /> </tool>