Mercurial > repos > iuc > vsnp_statistics

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
author iuc
date Fri, 10 Jun 2022 06:09:36 +0000
parents b960f47c57a1
children
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b960f47c57a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></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 <command detect_errors="exit_code"><![CDATA[
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7 #import re
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8
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9 #if $input_type_cond.input_type in ["single", "pair"]:
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10 #set read1 = $input_type_cond.read1
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11 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
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12 ln -s '${read1}' '${read1_identifier}' &&
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13 #set read1_seqkit_stats = $input_type_cond.read1_seqkit_stats
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14 #set read1_seqkit_fx2tab = $input_type_cond.read1_seqkit_fx2tab
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15 #if $input_type_cond.input_type == "pair":
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16 #set read2 = $input_type_cond.read2
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17 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
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18 ln -s '${read2}' '${read2_identifier}' &&
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19 #set read2_seqkit_stats = $input_type_cond.read2_seqkit_stats
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20 #set read2_seqkit_fx2tab = $input_type_cond.read2_seqkit_fx2tab
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21 #end if
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22 #else:
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23 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier))
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24 #set read1 = $input_type_cond.reads_collection.forward
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25 #set read1_identifier = $identifier + '_R1'
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26 ln -s '${read1}' '${read1_identifier}' &&
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27 #set read2 = $input_type_cond.reads_collection.reverse
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28 #set read2_identifier = $identifier + '_R2'
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29 ln -s '${read2}' '${read2_identifier}' &&
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30 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.seqkit_stats_collection.element_identifier))
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31 #set read1_seqkit_stats = $input_type_cond.seqkit_stats_collection.forward
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32 #set read2_seqkit_stats = $input_type_cond.seqkit_stats_collection.reverse
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33 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.seqkit_fx2tab_collection.element_identifier))
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34 #set read1_seqkit_fx2tab = $input_type_cond.seqkit_fx2tab_collection.forward
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35 #set read2_seqkit_fx2tab = $input_type_cond.seqkit_fx2tab_collection.reverse
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36 #end if
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37
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38 python '$__tool_directory__/vsnp_statistics.py'
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39 --read1 '${read1_identifier}'
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40 --read1_seqkit_stats '$read1_seqkit_stats'
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41 --read1_seqkit_fx2tab '$read1_seqkit_fx2tab'
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42 #if $input_type_cond.input_type in ['pair', 'paired']:
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43 --read2 '${read2_identifier}'
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44 --read2_seqkit_stats '$read2_seqkit_stats'
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45 --read2_seqkit_fx2tab '$read2_seqkit_fx2tab'
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46 #end if
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47 --output '$output'
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48 ]]></command>
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49 <inputs>
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50 <conditional name="input_type_cond">
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51 <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
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52 <option value="single" selected="true">Single files</option>
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53 <option value="paired">Paired reads</option>
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54 <option value="pair">Paired reads in separate data sets</option>
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55 </param>
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56 <when value="single">
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57 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
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58 <param name="read1_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected Fastq file"/>
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59 <param name="read1_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected Fastq file"/>
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60 </when>
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61 <when value="paired">
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62 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
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63 <param name="seqkit_stats_collection" type="data_collection" format="tabular" collection_type="paired" label="Collection of paired SeqKit statistics files"/>
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64 <param name="seqkit_fx2tab_collection" type="data_collection" format="tabular" collection_type="paired" label="Collection of paired SeqKit fx2tab files"/>
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65 </when>
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66 <when value="pair">
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67 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward read fastq file"/>
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68 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse read fastq file"/>
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69 <param name="read1_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected forward read"/>
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70 <param name="read2_seqkit_stats" type="data" format="tabular" label="SeqKit statistics file for selected reverse read"/>
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71 <param name="read1_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected forward read"/>
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72 <param name="read2_seqkit_fx2tab" type="data" format="tabular" label="SeqKit fx2tab file for selected reverse read"/>
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73 </when>
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74 </conditional>
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75 </inputs>
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76 <outputs>
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77 <data name="output" format="tabular"/>
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78 </outputs>
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79 <tests>
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80 <!-- A single fastq file -->
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81 <test expect_num_outputs="1">
2
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82 <param name="input_type" value="single"/>
4
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83 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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84 <param name="read1_seqkit_stats" value="r1_seqkit_stats1.tabular" ftype="tabular"/>
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85 <param name="read1_seqkit_fx2tab" value="r1_seqkit_fx2tab1.tabular" ftype="tabular"/>
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86 <output name="output" file="statistics_output1.tabular" ftype="tabular"/>
0
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87 </test>
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88 <!-- A set of paired fastq files -->
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89 <test expect_num_outputs="1">
2
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90 <param name="input_type" value="pair"/>
4
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91 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
a2f69b1598e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit c38fd63f7980c70390d104a73ba4c72b266444c3
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92 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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93 <param name="read1_seqkit_stats" value="r1_seqkit_stats2.tabular" ftype="tabular"/>
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94 <param name="read2_seqkit_stats" value="r2_seqkit_stats2.tabular" ftype="tabular"/>
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95 <param name="read1_seqkit_fx2tab" value="r1_seqkit_fx2tab2.tabular" ftype="tabular"/>
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96 <param name="read2_seqkit_fx2tab" value="r2_seqkit_fx2tab2.tabular" ftype="tabular"/>
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97 <output name="output" file="statistics_output2.tabular" ftype="tabular"/>
0
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98 </test>
2
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99 <!-- A collection of paired fastq files -->
0
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100 <test expect_num_outputs="1">
2
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101 <param name="input_type" value="paired"/>
0
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102 <param name="reads_collection">
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103 <collection type="paired">
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104 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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105 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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106 </collection>
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107 </param>
4
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108 <param name="seqkit_stats_collection">
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109 <collection type="paired">
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110 <element name="forward" value="r1_seqkit_stats2.tabular" ftype="tabular"/>
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111 <element name="reverse" value="r2_seqkit_stats2.tabular" ftype="tabular"/>
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112 </collection>
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113 </param>
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114 <param name="seqkit_fx2tab" value="seqkit_fx2tab3.tabular" ftype="tabular"/>
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115 <param name="seqkit_fx2tab_collection">
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116 <collection type="paired">
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117 <element name="forward" value="r1_seqkit_fx2tab2.tabular" ftype="tabular"/>
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118 <element name="reverse" value="r2_seqkit_fx2tab2.tabular" ftype="tabular"/>
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119 </collection>
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120 </param>
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121 <output name="output" file="statistics_output3.tabular" ftype="tabular"/>
0
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122 </test>
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123 </tests>
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124 <help>
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125 **What it does**
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126
4
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127 Accepts fastq samples and SeqKit stats and fx2tab files produced from the samples and extracts information from them to produce a tabular
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128 file containing statistics for each sample. The samples can be a single read, a single set of paired reads in separate datasets or a
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129 collection of paired reas. The output statistics include file size, read count, sum / avg / max read length, Q1, Q2, Q3, sum gap, N50,
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130 reads passing Q20 / Q30, and average read quality.
0
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131 </help>
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132 <expand macro="citations"/>
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133 </tool>
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134