Mercurial > repos > iuc > stacks2_kmerfilter
diff stacks_kmerfilter.xml @ 0:b2e3553e1be2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 10:58:28 -0400 |
parents | |
children | 38c9f9a680f0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_kmerfilter.xml Mon Jul 01 10:58:28 2019 -0400 @@ -0,0 +1,200 @@ +<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>