Mercurial > repos > cpt > cpt_search_file

annotate searchFile.xml @ 2:21ae0e340d80 draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:22 +0000
parents 6e3a843b6304
children
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1 <tool id="edu.tamu.cpt.proximity.searchFile" name="Search File" version="1.0">
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2 <description>Queries a gff3, genbank, fasta, or blastxml file for a user defined set of terms</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="0.10.1">gffutils</requirement>
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9 </expand>
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10 <command detect_errors="aggressive"><![CDATA[
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11 python2.7 '$__tool_directory__/searchFile.py'
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12 #if $check is not None:
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13 --dbaseTerms "$check"
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14 #end if
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15 #if $term_add.term_selector == "customtxt":
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16 --custom_txt "$term_add.custom_txt"
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17 #elif $term_add.term_selector == "customfile":
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18 --custom_file "$term_add.custom_file"
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19 #else:
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20 #pass
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21 #end if
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22 #for $input_select in $input_files:
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23 #if $input_select.file_selector.file_select == "gff3selection":
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24 --gff3_files #for $gff3_file in $input_select.file_selector.gff3_files:
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25 "${gff3_file}" #end for
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26 #end if
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27 #if $input_select.file_selector.file_select == "gbkselection":
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28 --gbk_files #for $gbk_file in $input_select.file_selector.gbk_files:
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29 "${gbk_file}" #end for
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30 #end if
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31 #if $input_select.file_selector.file_select == "faselection":
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32 --fa_files #for $fa_file in $input_select.file_selector.fa_files:
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33 "${fa_file}" #end for
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34 #end if
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35 #if $input_select.file_selector.file_select == "blastselection":
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36 --blast_files #for $blast_file in $input_select.file_selector.blast_files:
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37 "${blast_file}" #end for
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38 #end if
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39 #end for
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40 #if $prox:
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41 --prox
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42 #end if
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43 --output '$output'
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44 ]]></command>
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45 <inputs>
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46 <param label="Using Proximity to Lysis Pipeline?" name="prox" type="boolean" truevalue="--prox" falsevalue="" checked="false" help="required GFF3 input"/>
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47 <param name="check" type="select" format="text" optional="true" label="Family terms to search" multiple="true" help="Terms avilable to query from the Lysis-family synonym database (see terms in Shared Data/Lysis family Terms)" display="checkboxes">
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48 <option value="endolysins" selected="true">Endolysins</option>
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49 <option value="holins" selected="true">Holins and Anti-holins</option>
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50 <option value="spanins" selected="true">Spanins</option>
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51 <option value="endolysin_domains" selected="true">Endolysin Associated Domains</option>
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52 <option value="spanin_domains" selected="true">Spanin Associated Domains</option>
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53 <option value="holin_domains" selected="true">Holin Associated Domains</option>
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54 </param>
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55 <conditional name="term_add">
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56 <param name="term_selector" type="select" label="Choose if you'd like to add custom terms">
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57 <option value="nocustom" selected="false">No Custom Terms</option>
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58 <option value="customtxt" selected="false">Custom Text</option>
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59 <option value="customfile" selected="false">Custom File</option>
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60 </param>
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61 <when value="customtxt">
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62 <param name="custom_txt" label="Custom Text" optional="true" type="text" area="true" help="Custom text box for search terms, must be separated by newline (enter)"/>
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63 </when>
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64 <when value="customfile">
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65 <param name="custom_file" label="Custom File" optional="true" type="data" format="txt" help="Custom search terms, uploaded via file, where terms must be separated by newline"/>
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66 </when>
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67 </conditional>
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68 <repeat name="input_files" title="Input Files">
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69 <conditional name="file_selector">
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70 <param name="file_select" type="select" label="Choose the type of file(s) you'd like to query">
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71 <option value="gff3selection" selected="false">GFF3</option>
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72 <option value="gbkselection" selected="false">Genbank</option>
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73 <option value="faselection" selected="false">FASTA</option>
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74 <option value="blastselection" selected="false">BLAST-XML</option>
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75 </param>
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76 <when value="gff3selection">
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77 <param name="gff3_files" label="GFF3 Input" optional="true" multiple="true" type="data" format="gff3"/>
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78 </when>
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79 <when value="gbkselection">
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80 <param name="gbk_files" label="Genbank Input" optional="true" multiple="true" type="data" format="genbank"/>
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81 </when>
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82 <when value="faselection">
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83 <param name="fa_files" label="FASTA Input" optional="true" multiple="true" type="data" format="fasta"/>
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84 </when>
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85 <when value="blastselection">
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86 <param name="blast_files" label="BLAST-xml Input" optional="true" multiple="true" type="data" format="xml"/>
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87 </when>
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88 </conditional>
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89 </repeat>
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90 </inputs>
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91 <outputs>
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92 <data format="txt" name="output" label="termHits">
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93 <change_format>
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94 <when input="prox" value="--prox" format="gff3"/>
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95 </change_format>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="prox" value="--prox"/>
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101 <param name="check" value="spanins"/>
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102 <repeat name="input_files">
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103 <conditional name="file_selector">
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104 <param name="file_select" value="gff3selection"/>
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105 <param name="gff3_files" value="lambda_spaninBLAST.gff3"/>
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106 </conditional>
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107 </repeat>
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108 <output name="output" file="termHits"/>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
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112 INPUT : A user's file(s) of interest (gff3, gbk, fasta, or blast-xml) and query said file(s) with a determined set of search terms. The search terms can be either from the curated lysis synonym database, and/or a custom input via file or text box. Additionally, if a user is performing this script in the proximity to lysis workflow, the selector needs to be selected to true, and only gff3 files will be able to complete the job.
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113
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114 OUTPUT : "termHits.txt" output file has file-type separated returns for features, or lines, that contained hits to a query term. See file search areas, for the regions of each type of file that are searched. If used for the proximity to lysis workflow, the output will be a proxHits.gff3 file that will be able to be fed to the next stages of the pipeline.
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115
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116 DBase Family Term Descriptions :
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117
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118 - Endolysins: enzymes that attack one of the structural bonds of the peptidoglycan. The endolysin step requires the hole-forming function of the holins.
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119
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120 - Holins and Anti-holins: small cytoplasmic membrane proteins that control the timing of lysis by forming a lethal membrane hole at a programmed time (programmed into the holin itself).
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121
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122 - Spanins: A periplasm-spanning protein complex that disrupts the outer membrane of the host in phage lysis. These complexes are currently identified as either a unimolecular spanin (u-spanin) or two-component system (i-spanin and o-spanin pair).
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123
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124 - Endolysins Domains: information pulled from PMID: 30873139
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125
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126 - Spanin Domains: information pulled from http://www.ebi.ac.uk/interpro/search/text/spanin/
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127
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128 - Holin Domains: information pulled from http://www.ebi.ac.uk/interpro/search/text/holin/
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129
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130 Additionally, some terms were added by querying QuickGO, located at https://www.ebi.ac.uk/QuickGO/
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131
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132 File Search Areas:
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133
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134 - gff3 : entire row
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135
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136 - genbank : product and note qualifier of each feature
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137
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138 - fasta : header field
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139
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140 - blast-xml : hit description
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141 ]]></help>
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142 <citations>
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143 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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144 <citation type="bibtex">
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145 @unpublished{galaxyTools,
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146 author = {C. Ross},
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147 title = {CPT Galaxy Tools},
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148 year = {2020-},
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149 note = {https://github.com/tamu-cpt/galaxy-tools/}
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150 }
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151 </citation>
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152 </citations>
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153 </tool>