Mercurial > repos > iuc > mykrobe_predict

annotate mykrobe_predict.xml @ 5:db95e63ac3fb draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:46:02 +0000
parents 70a3a5377e6d
children
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1 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0" profile="@PROFILE@">
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2 <description>Antibiotic resistance predictions</description>
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3 <xrefs>
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4 <xref type="bio.tools">Mykrobe</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macro.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import difflib
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12 #import re
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14 mykrobe predict
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15 --species '${select_species.species}'
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16 --panel '${select_species.panel}'
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17
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18 #if $conf_percent_cutoff:
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19 --conf_percent_cutoff '${conf_percent_cutoff}'
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20 #end if
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21
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22 #if $min_depth:
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23 --min_depth ${min_depth}
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24 #end if
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26 @shared_options@
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28 -q
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29 -t "\${GALAXY_SLOTS:-1}"
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31 #if $data_type.type in ["single", "paired"]:
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32 #set read1 = $data_type.seq1
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33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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34 #if $data_type.type == "single":
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35 --sample '${read1_identifier}'
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36 --seq '${read1}'
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37 #else:
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38 #set read2 = $data_type.seq2
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39 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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40 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
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41 #set match = $matches[0]
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42 #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
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43 --sample '${identifier}'
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44 --seq '${read1}' '${read2}'
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45 #end if
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46 #elif $data_type.type == "collection":
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47 #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier))
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48 --sample '${identifier}'
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49 --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}'
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50 #end if
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51
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52 --format '${format}'
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53
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54 > '$output']]>
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55 </command>
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56 <inputs>
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57 <expand macro="inputs"/>
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58 <conditional name="select_species">
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59 <param name="species" type="select" label="Specify Species for AMR">
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60 <option value="tb">Mycobacterium tuberculosis (tb)</option>
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61 <option value="staph">Staphylococcus aureus (staph)</option>
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62 <option value="sonnei">Shigella sonnei (sonnei)</option>
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63 </param>
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64 <when value="staph">
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65 <param name="panel" type="select" label="Select panel for Staph only">
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66 <option value="20170217">20170217</option>
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67 </param>
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68 </when>
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69 <when value="tb">
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70 <param name="panel" type="select" label="Select panel for TB only">
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71 <option value="202010">202010</option>
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72 <option value="201901">201901</option>
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73 <option value="bradley-2015">Bradely 2015</option>
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74 </param>
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75 </when>
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76 <when value="sonnei">
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77 <param name="panel" type="select" label="Select panel for sonnei only">
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78 <option value="20210201">20210201</option>
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79 <option value="20201012">20201012</option>
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80 </param>
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81 </when>
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82 </conditional>
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83 <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/>
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84 <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff">
70a3a5377e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
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85 <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
3
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86 </param>
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87 <expand macro="options"/>
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88 <param argument="--format" type="select" label="Select the prefered output format">
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89 <option value="csv" >csv</option>
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90 <option value="json">json</option>
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91 </param>
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92 </inputs>
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93 <outputs>
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94 <data name="output" format="csv" label="prediction">
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95 <change_format>
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96 <when input="format" value="json" format="json"/>
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97 </change_format>
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98 </data>
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="type" value="single"/>
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103 <param name="seq1" ftype="fastq" value="reads.fastq"/>
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104 <param name="species" value="tb"/>
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105 <param name="panel" value="bradley-2015"/>
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106 <param name="format" value="json"/>
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107 <output name="output">
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108 <assert_contents>
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109 <has_text_matching expression="susceptibility"/>
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110 </assert_contents>
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111 </output>
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112 </test>
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113 <test>
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114 <param name="type" value="single"/>
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115 <param name="seq1" ftype="fastq" value="reads.fastq"/>
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116 <param name="species" value="sonnei"/>
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117 <param name="panel" value="20201012"/>
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118 <param name="format" value="json"/>
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119 <output name="output">
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120 <assert_contents>
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121 <has_text_matching expression="susceptibility"/>
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122 </assert_contents>
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123 </output>
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124 </test>
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125 <test>
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126 <param name="type" value="single"/>
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127 <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
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128 <param name="species" value="sonnei"/>
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129 <param name="panel" value="20201012"/>
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130 <param name="format" value="json"/>
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131 <output name="output">
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132 <assert_contents>
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133 <has_text_matching expression="susceptibility"/>
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134 </assert_contents>
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135 </output>
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136 </test>
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137 </tests>
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138 <help>
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139 @ATTRIBUTION@
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140 </help>
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141 <expand macro="citation" />
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142 </tool>
4
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143