Mercurial > repos > galaxyp > filter_by_fasta_ids

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 03:18:11 -0400
parents cd22452edec2
children
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5
dff7df6fcab5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
galaxyp
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1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.3">
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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2 <description>on the headers and/or the sequences</description>
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3 <macros>
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4 <xml name="regexp_macro" token_label="Regular expression pattern">
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5 <param name="regexp" type="text" value="" label="@LABEL@" help="Use the Python regular expression syntax as specified in https://docs.python.org/3/library/re.html">
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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6 <validator type="empty_field" />
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7 <sanitizer>
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8 <valid initial="string.printable">
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9 <remove value="'"/>
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10 </valid>
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11 <mapping initial="none">
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12 <add source="'" target="'&quot;'&quot;'" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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13 </mapping>
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14 </sanitizer>
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15 </param>
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16 </xml>
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17 </macros>
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18 <requirements>
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19 <requirement type="package" version="3.6.5">python</requirement>
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20 </requirements>
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21 <command><![CDATA[
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22 python '$__tool_directory__/filter_by_fasta_ids.py'
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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23 -i '$input'
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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24 #if $header_criteria.header_criteria_select == 'id_list'
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25 --id_list '$header_criteria.identifiers'
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26 #if $header_criteria.id_regex.find == 'pattern':
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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27 --pattern '$header_criteria.id_regex.pattern'
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cd22452edec2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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28 #else:
cd22452edec2 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
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29 --pattern '>([^| ]+)'
3
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30 #end if
2
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31 #elif $header_criteria.header_criteria_select == 'regexp'
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32 --header_regexp '$header_criteria.regexp'
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33 #end if
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34 #if $sequence_criteria.sequence_criteria_select == 'seq_length'
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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35 --min_length $sequence_criteria.min_length
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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36 #if str($sequence_criteria.max_length)
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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37 --max_length $sequence_criteria.max_length
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38 #end if
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39 #elif $sequence_criteria.sequence_criteria_select == 'regexp'
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40 --sequence_regexp '$sequence_criteria.regexp'
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41 #end if
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42 $dedup
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43 -o '$output'
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44 #if $output_discarded
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45 -d '$discarded'
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46 #end if
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47 ]]></command>
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48 <inputs>
2
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49 <param name="input" type="data" format="fasta" label="FASTA sequences"/>
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50 <conditional name="header_criteria">
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51 <param name="header_criteria_select" type="select" label="Criteria for filtering on the headers">
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52 <option value="">No filtering</option>
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53 <option value="id_list">List of IDs</option>
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54 <option value="regexp">Regular expression on the headers</option>
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55 </param>
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56 <when value="" />
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57 <when value="id_list">
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58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/>
3
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59 <conditional name="id_regex">
4
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60 <param name="find" type="select" label="Match IDs by"
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61 help="Default: &gt;ID will use search pattern >([^| ]+) to input ID; Use custom regex to change">
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62 <option value="beginning">Default: ID is expected at the beginning: &gt;ID </option>
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63 <option value="pattern">Custom regex pattern</option>
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64 </param>
4
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65 <when value="beginning" />
3
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66 <when value="pattern">
4
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67 <param name="pattern" type="text" value="" label="Regex search pattern for ID"
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68 help="Search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$">
3
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69 <sanitizer sanitize="False"/>
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70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator>
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71 </param>
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72 </when>
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73 </conditional>
2
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74 </when>
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75 <when value="regexp">
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76 <expand macro="regexp_macro" label="Regular expression pattern the header should match" />
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77 </when>
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78 </conditional>
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79 <conditional name="sequence_criteria">
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80 <param name="sequence_criteria_select" type="select" label="Criteria for filtering on the sequences">
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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81 <option value="">No filtering</option>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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82 <option value="seq_length">Sequence length</option>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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83 <option value="regexp">Regular expression on the sequences</option>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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84 </param>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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85 <when value="" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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86 <when value="seq_length">
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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87 <param name="min_length" type="integer" value="0" label="Minimum length" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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88 <param name="max_length" type="integer" min="1" value="" optional="true" label="Maximum length" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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89 </when>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
galaxyp
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90 <when value="regexp">
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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91 <expand macro="regexp_macro" label="Regular expression pattern the sequence should match" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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92 </when>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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93 </conditional>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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94 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" label="Remove duplicate sequences" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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95 <param name="output_discarded" type="boolean" label="Output discarded FASTA entries" />
1
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96 </inputs>
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97 <outputs>
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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98 <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA sequences"/>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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99 <data name="discarded" format="fasta" label="${tool.name} on ${on_string}: discarded entries">
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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100 <filter>output_discarded</filter>
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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101 </data>
1
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102 </outputs>
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103 <tests>
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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104 <test expect_num_outputs="1">
1
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105 <param name="input" ftype="fasta" value="input.fasta" />
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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106 <param name="header_criteria_select" value="id_list" />
1
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107 <param name="identifiers" ftype="txt" value="ids.txt" />
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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108 <param name="dedup" value="True" />
1
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109 <output name="output" file="output_dedup.fasta" />
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110 </test>
3
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111 <test expect_num_outputs="1">
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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112 <param name="input" ftype="fasta" value="input_sp.fasta" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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113 <param name="header_criteria_select" value="id_list" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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114 <param name="find" value="pattern" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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115 <param name="pattern" value=">.+?\|(.+?)\|.*$" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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116 <param name="identifiers" ftype="txt" value="ids_sp.txt" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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117 <param name="dedup" value="True" />
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118 <output name="output" file="output_sp_dedup.fasta" />
3c623e81be77 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
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119 </test>
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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120 <test expect_num_outputs="2">
1
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121 <param name="input" ftype="fasta" value="input.fasta" />
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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122 <param name="header_criteria_select" value="id_list" />
1
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123 <param name="identifiers" ftype="txt" value="ids.txt" />
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124 <param name="dedup" value="False" />
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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125 <param name="output_discarded" value="True" />
1
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126 <output name="output" file="output_not_dedup.fasta" />
2
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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127 <output name="discarded" file="discarded_not_dedup.fasta" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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128 </test>
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129 <test expect_num_outputs="2">
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130 <param name="input" ftype="fasta" value="input.fasta" />
4
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131 <conditional name="header_criteria">
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132 <param name="header_criteria_select" value="regexp" />
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133 <param name="regexp" value="2" />
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134 </conditional>
2
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135 <param name="dedup" value="False" />
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136 <param name="output_discarded" value="True" />
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137 <output name="output" file="output_header_regexp.fasta" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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138 <output name="discarded" file="discarded_header_regexp.fasta" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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139 </test>
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140 <test expect_num_outputs="2">
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141 <param name="input" ftype="fasta" value="input.fasta" />
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142 <param name="sequence_criteria_select" value="seq_length" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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143 <param name="min_length" value="5" />
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144 <param name="dedup" value="False" />
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145 <param name="output_discarded" value="True" />
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146 <output name="output" file="output_min_length5.fasta" />
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147 <output name="discarded" file="discarded_min_length5.fasta" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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148 </test>
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149 <test expect_num_outputs="2">
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150 <param name="input" ftype="fasta" value="input.fasta" />
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151 <param name="sequence_criteria_select" value="seq_length" />
1bd985f14938 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
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152 <param name="max_length" value="4" />
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153 <param name="dedup" value="False" />
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154 <param name="output_discarded" value="True" />
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155 <output name="output" file="output_max_length4.fasta" />
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156 <output name="discarded" file="discarded_max_length4.fasta" />
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157 </test>
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158 <test expect_num_outputs="2">
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159 <param name="input" ftype="fasta" value="input.fasta" />
4
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160 <conditional name="sequence_criteria">
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161 <param name="sequence_criteria_select" value="regexp" />
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162 <param name="regexp" value="T{2,}" />
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163 </conditional>
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164 <param name="dedup" value="False" />
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165 <param name="output_discarded" value="True" />
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166 <output name="output" file="output_sequence_regexp.fasta" />
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167 <output name="discarded" file="discarded_sequence_regexp.fasta" />
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168 </test>
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169 <test expect_num_outputs="2">
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170 <param name="input" ftype="fasta" value="input.fasta" />
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171 <conditional name="header_criteria">
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172 <param name="header_criteria_select" value="regexp" />
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173 <param name="regexp" value="3|5" />
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174 </conditional>
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175 <conditional name="sequence_criteria">
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176 <param name="sequence_criteria_select" value="regexp" />
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177 <param name="regexp" value="ACGT" />
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178 </conditional>
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179 <param name="dedup" value="False" />
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180 <param name="output_discarded" value="True" />
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181 <output name="output" file="output_header_regexp_sequence_regexp.fasta" />
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182 <output name="discarded" file="discarded_header_regexp_sequence_regexp.fasta" />
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186 **What it does**
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187
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188 Filter entries of a FASTA file on the headers and/or the sequences based on various criteria.
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189 ]]></help>
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190 </tool>