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annotate cryptogenotyper.xml @ 1:d4a96287909e draft default tip

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"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 232da91ef9014d518a1c14dac403961bfb9223cf"
author nml
date Fri, 16 Oct 2020 22:32:56 +0000
parents 06afaa20dd23
children
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d4a96287909e "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 232da91ef9014d518a1c14dac403961bfb9223cf"
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1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
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2 <description>
1
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3 classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
0
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4 </description>
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5 <macros>
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6 <token name="@VERSION@">1.0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement>
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10 </requirements>
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11 <version_command>cryptogenotyper --version</version_command>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14
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15 #set $ref_file=''
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16
1
d4a96287909e "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 232da91ef9014d518a1c14dac403961bfb9223cf"
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17 #if $db
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18 ln -s '${db}' '${db.name}' &&
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19 #set $ref_file = $db.name
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20 #end if
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21
1
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22 #if $primers['seqtype'] == 'contig'
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23 ln -s '${$primers.abi_input['forward']}' '${primers.abi_input.name}_forward.ab1' &&
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24 ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' &&
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25 cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
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26 #if $db
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27 --databasefile $ref_file
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28 #end if
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29 #else
1
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30 ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' &&
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31 cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype'
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32 #if $db
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33 --databasefile $ref_file
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34 #end if
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35 #end if
1
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36 $outputheader
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37 -o 'result'
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="marker" type="select" label="Marker">
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42 <option value="18S">SSU rRNA</option>
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43 <option value="gp60">gp60</option>
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44 </param>
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45 <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
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46 <conditional name="primers">
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47 <param name="seqtype" type="select" label="Type of Sequences">
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48 <option value="forward">Forward Only</option>
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49 <option value="reverse">Reverse Only</option>
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50 <option selected="true" value="contig">Contig</option>
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51 </param>
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52 <when value="contig">
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53 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/>
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54 </when>
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55 <when value="forward">
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56 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/>
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57 </when>
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58 <when value="reverse">
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59 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/>
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60 </when>
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61 </conditional>
1
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62 <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
0
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63 </param>
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64
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65
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66 </inputs>
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67 <outputs>
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68 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>
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69 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/>
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70 </outputs>
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71
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72 <tests>
1
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73 <test expect_num_outputs="2">
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74 <param name="marker" value="18S"/>
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75 <param name="seqtype" value="forward"/>
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76 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
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77 <output name="outfile_report" ftype="tabular">
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78 <assert_contents>
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79 <has_text_matching expression="C.parvum"/>
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80 </assert_contents>
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81 </output>
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82 </test>
1
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83 <test expect_num_outputs="2">
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84 <param name="marker" value="gp60"/>
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85 <param name="seqtype" value="forward"/>
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86 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
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87 <output name="outfile_report" ftype="tabular" >
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88 <assert_contents>
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89 <has_text_matching expression="C.parvum"/>
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90 </assert_contents>
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91 </output>
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92 </test>
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93 </tests>
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94
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95
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96 <help>
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97
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98
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99 **Syntax**
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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100
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101 CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.
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102 For more information please visit https://github.com/phac-nml/CryptoGenotyper.
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103
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104 -----
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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105
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106 **Input:**
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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107
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108 AB1 file(s) representing *Cryptosporidium's* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)).
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109 Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification.
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110
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111
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112 **Output:**
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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113
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114 FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample.
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115 </help>
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116 <citations>
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117 <citation type="bibtex">
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118 @misc{githubCryptoGenotyper,
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119 author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R},
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120 title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
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121 publisher = {GitHub},
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122 journal = {GitHub repository},
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123 url = {https://github.com/phac-nml/CryptoGenotyper}
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124 }</citation>
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125 </citations>
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126
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127 </tool>