Mercurial > repos > iuc > qiime_filter_fasta

annotate filter_fasta.xml @ 7:03469c9daff1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 07:40:53 -0500
parents 82ab467a74fc
children
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03469c9daff1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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1 <tool id="qiime_filter_fasta" name="Filter fasta" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
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2 <description>to remove sequences based on input criteria (filter_fasta)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive"><![CDATA[
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03469c9daff1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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8 @MPLBACKEND@
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9 filter_fasta.py
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10 --input_fasta_fp '$input_fasta_fp'
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11 --output_fasta_fp '$fitered_fasta'
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12 #if $selection.type == "otu_map"
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13 --otu_map '$selection.otu_map'
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14 #else if $selection.type == "seq_list"
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15 --seq_id_fp '$selection.seq_id_fp'
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16 #else if $selection.type == "biom"
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17 --biom_fp '$selection.biom_fp'
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18 #else if $selection.type == "fasta"
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19 --subject_fasta_fp '$selection.subject_fasta_fp'
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20 #else if $selection.type == "prefix"
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21 --seq_id_prefix '$selection.seq_id_prefix'
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22 #else if $selection.type == "prefix_list"
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23 --sample_id_fp '$selection.sample_id_fp'
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24 #else if $selection.type == "valid_states"
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25 --mapping_fp '$selection.mapping_fp'
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26 --valid_states '$selection.valid_states'
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27 #end if
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28 $negate
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29 ]]></command>
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30 <inputs>
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31 <param name="input_fasta_fp" argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/>
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32 <conditional name="selection">
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33 <param name="type" label="Type of criteria for filtering" type="select">
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34 <option value="otu_map">OTU map-based filtering</option>
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35 <option value="seq_list">Filtering using a list of sequence identifiers</option>
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36 <option value="biom">Filtering based on OTU identifiers in a BIOM file</option>
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37 <option value="fasta">Filtering based on sequence identifiers in a Fasta file</option>
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38 <option value="prefix">Filtering based on a sequence id prefix</option>
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39 <option value="prefix_list">Filtering based on a list of sequence id prefix</option>
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40 <option value="valid_states">Filtering based on a sample id description</option>
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41 </param>
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42 <when value="otu_map">
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43 <param argument="--otu_map" type="data" format="txt" label="OTU map where sequences ids are those which should be retained"/>
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44 </when>
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45 <when value="seq_list">
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46 <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"/>
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47 </when>
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48 <when value="biom">
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49 <param argument="--biom_fp" type="data" format="biom1" label="Biom file with OTU identifiers that should be retained"/>
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50 </when>
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51 <when value="fasta">
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52 <param argument="--subject_fasta_fp" type="data" format="fasta" label="Fasta file where the seq ids should be retained"/>
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53 </when>
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54 <when value="prefix">
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55 <param argument="--seq_id_prefix" type="text" label="Prefix to keep seqs where seq_id starts with this prefix"/>
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56 </when>
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57 <when value="prefix_list">
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58 <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"/>
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59 </when>
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60 <when value="valid_states">
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61 <param argument="--mapping_fp" type="data" format="txt" label="Mapping file"/>
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62 <param argument="--valid_states" type="text" label="Description of the sample ids to retain"/>
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63 </when>
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64 </conditional>
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65 <param argument="--negate" type="boolean" truevalue="--negate" falsevalue="" checked="false" label="Discard passed seq ids rather than keep passed seq ids?"/>
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66 </inputs>
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67 <outputs>
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68 <data name="fitered_fasta" format="fasta" label="${tool.name} on ${on_string}: Filtered sequences"/>
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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73 <param name="type" value="otu_map"/>
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74 <param name="otu_map" value="filter_fasta/otu_map.txt"/>
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75 <param name="negate" value=""/>
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76 <output name="fitered_fasta" md5="9185f3cdcba8bcaf159cc3f1fdbb5ebb"/>
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77 </test>
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78 <test>
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79 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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80 <param name="type" value="otu_map"/>
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81 <param name="otu_map" value="filter_fasta/otu_map.txt"/>
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82 <param name="negate" value="--negate"/>
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83 <output name="fitered_fasta" md5="206a5c83e5abbd674f632da73ec518a2"/>
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84 </test>
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85 <test>
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86 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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87 <param name="type" value="seq_list"/>
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88 <param name="seq_id_fp" value="filter_fasta/seqs_to_keep.txt"/>
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89 <param name="negate" value=""/>
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90 <output name="fitered_fasta" md5="19ba95928ca9419f671810240120c8cd"/>
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91 </test>
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92 <test>
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93 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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94 <param name="type" value="biom"/>
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95 <param name="biom_fp" value="filter_fasta/otu_table.biom"/>
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96 <param name="negate" value=""/>
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97 <output name="fitered_fasta" md5="d41d8cd98f00b204e9800998ecf8427e"/>
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98 </test>
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99 <test>
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100 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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101 <param name="type" value="fasta"/>
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102 <param name="subject_fasta_fp" value="filter_fasta/sl_inseqs.fasta"/>
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103 <param name="negate" value=""/>
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104 <output name="fitered_fasta" md5="9c5f416e94bcfb2d4003ea002cbaf617"/>
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105 </test>
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106 <test>
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107 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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108 <param name="type" value="prefix"/>
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109 <param name="seq_id_prefix" value="S5"/>
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110 <param name="negate" value=""/>
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111 <output name="fitered_fasta" md5="c1f2d8c5844733f30ca07547846c4d36"/>
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112 </test>
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113 <test>
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114 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/>
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115 <param name="type" value="prefix_list"/>
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116 <param name="sample_id_fp" value="filter_fasta/map.txt"/>
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117 <param name="negate" value=""/>
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118 <output name="fitered_fasta" md5="8f0025b067d22ed708ee55de10016785"/>
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119 </test>
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120 </tests>
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121 <help><![CDATA[
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122 **What it does**
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123
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124 Filter fasta or fastq file to remove sequences based on input criteria
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125 ]]></help>
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126 <citations>
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127 <expand macro="citations"/>
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128 </citations>
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129 </tool>