Mercurial > repos > iuc > qiime_filter_fasta
diff filter_fasta.xml @ 0:794553858db3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:38:13 -0400 |
| parents | |
| children | 82ab467a74fc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_fasta.xml Thu May 18 09:38:13 2017 -0400 @@ -0,0 +1,128 @@ +<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>