Mercurial > repos > iuc > qiime_filter_fasta
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author | iuc |
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date | Thu, 18 May 2017 09:38:13 -0400 |
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children | 82ab467a74fc |
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<tool id="qiime_filter_fasta" name="Filter fasta" version="@WRAPPER_VERSION@.0"> <description>to remove sequences based on input criteria</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ filter_fasta.py --input_fasta_fp '$input_fasta_fp' --output_fasta_fp '$fitered_fasta' #if $selection.type == "otu_map" --otu_map '$selection.otu_map' #else if $selection.type == "seq_list" --seq_id_fp '$selection.seq_id_fp' #else if $selection.type == "biom" --biom_fp '$selection.biom_fp' #else if $selection.type == "fasta" --subject_fasta_fp '$selection.subject_fasta_fp' #else if $selection.type == "prefix" --seq_id_prefix '$selection.seq_id_prefix' #else if $selection.type == "prefix_list" --sample_id_fp '$selection.sample_id_fp' #else if $selection.type == "valid_states" --mapping_fp '$selection.mapping_fp' --valid_states '$selection.valid_states' #end if $negate ]]></command> <inputs> <param name="input_fasta_fp" argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/> <conditional name="selection"> <param name="type" label="Type of criteria for filtering" type="select"> <option value="otu_map">OTU map-based filtering</option> <option value="seq_list">Filtering using a list of sequence identifiers</option> <option value="biom">Filtering based on OTU identifiers in a BIOM file</option> <option value="fasta">Filtering based on sequence identifiers in a Fasta file</option> <option value="prefix">Filtering based on a sequence id prefix</option> <option value="prefix_list">Filtering based on a list of sequence id prefix</option> <option value="valid_states">Filtering based on a sample id description</option> </param> <when value="otu_map"> <param argument="--otu_map" type="data" format="txt" label="OTU map where sequences ids are those which should be retained"/> </when> <when value="seq_list"> <param argument="--seq_id_fp" type="data" format="tabular,tsv,csv,txt" label="List of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/> </when> <when value="biom"> <param argument="--biom_fp" type="data" format="biom1" label="Biom file with OTU identifiers that should be retained"/> </when> <when value="fasta"> <param argument="--subject_fasta_fp" type="data" format="fasta" label="Fasta file where the seq ids should be retained"/> </when> <when value="prefix"> <param argument="--seq_id_prefix" type="text" label="Prefix to keep seqs where seq_id starts with this prefix"/> </when> <when value="prefix_list"> <param argument="--sample_id_fp" type="data" format="txt" label="List of prefix to keep seqs where seq_id starts with a sample id listed in this file"/> </when> <when value="valid_states"> <param argument="--mapping_fp" type="data" format="txt" label="Mapping file"/> <param argument="--valid_states" type="text" label="Description of the sample ids to retain"/> </when> </conditional> <param argument="--negate" type="boolean" truevalue="--negate" falsevalue="" checked="False" label="Discard passed seq ids rather than keep passed seq ids?"/> </inputs> <outputs> <data name="fitered_fasta" format="fasta" label="${tool.name} on ${on_string}: Filtered sequences"/> </outputs> <tests> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="otu_map"/> <param name="otu_map" value="filter_fasta/otu_map.txt"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="9185f3cdcba8bcaf159cc3f1fdbb5ebb"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="otu_map"/> <param name="otu_map" value="filter_fasta/otu_map.txt"/> <param name="negate" value="--negate"/> <output name="fitered_fasta" md5="206a5c83e5abbd674f632da73ec518a2"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="seq_list"/> <param name="seq_id_fp" value="filter_fasta/seqs_to_keep.txt"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="19ba95928ca9419f671810240120c8cd"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="biom"/> <param name="biom_fp" value="filter_fasta/otu_table.biom"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="d41d8cd98f00b204e9800998ecf8427e"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="fasta"/> <param name="subject_fasta_fp" value="filter_fasta/sl_inseqs.fasta"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="9c5f416e94bcfb2d4003ea002cbaf617"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="prefix"/> <param name="seq_id_prefix" value="S5"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="c1f2d8c5844733f30ca07547846c4d36"/> </test> <test> <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> <param name="type" value="prefix_list"/> <param name="sample_id_fp" value="filter_fasta/map.txt"/> <param name="negate" value=""/> <output name="fitered_fasta" md5="8f0025b067d22ed708ee55de10016785"/> </test> </tests> <help><![CDATA[ **What it does** Filter fasta or fastq file to remove sequences based on input criteria ]]></help> <citations> <expand macro="citations"/> </citations> </tool>