Mercurial > repos > nml > cryptogenotyper

annotate cryptogenotyper.xml @ 0:06afaa20dd23 draft

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"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
author nml
date Fri, 16 Oct 2020 02:23:24 +0000
parents
children d4a96287909e
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0
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@">
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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2 <description>
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3 CryptoGenotyper is a standalone tool to analyze Cryptosporidium Sanger sequencing data and classify the species and subtype based on SSU rRNA and gp60 gene markers, respectively.
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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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
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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17 #if $reference.ref == "no"
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18 ln -s "${reference.db}" "${reference.db.name}" &&
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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19 #set $ref_file = $reference.db.name
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20 #end if
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21
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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"
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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26 #if $reference.ref == "no"
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27 --databasefile $ref_file
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28 #end if
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29 #else
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30 ln -s "${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" -f "" -r ""
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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32 #if $reference.ref == "no"
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33 --databasefile $ref_file
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34 #end if
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35 #end if
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36 #if $outputheader == "no"
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37 --noheaderline
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38 #end if
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39 -o "result";
06afaa20dd23 "planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
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40 ]]>
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41 </command>
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42 <inputs>
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43 <param name="marker" type="select" label="Marker">
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44 <option value="18S">SSU rRNA</option>
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45 <option value="gp60">gp60</option>
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46 </param>
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47 <conditional name="reference">
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48 <param name="ref" type="select" label="Use default reference file?">
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49 <option value="yes">Yes</option>
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50 <option value="no">No</option>
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51 </param>
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52 <when value="yes">
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53 </when>
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54 <when value="no">
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55 <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/>
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56 </when>
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57 </conditional>
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58 <conditional name="primers">
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59 <param name="seqtype" type="select" label="Type of Sequences">
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60 <option value="forward">Forward Only</option>
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61 <option value="reverse">Reverse Only</option>
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62 <option selected="true" value="contig">Contig</option>
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63 </param>
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64 <when value="contig">
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65 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/>
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66 </when>
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67 <when value="forward">
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68 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/>
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69 </when>
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70 <when value="reverse">
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71 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/>
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72 </when>
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73 </conditional>
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74 <param name="outputheader" type="select" value="yes" label="Output header line in the report?">
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75 <option value="yes">Yes</option>
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76 <option value="no">No</option>
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77 </param>
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78
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79
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80 </inputs>
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81 <outputs>
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82 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/>
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83 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/>
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <param name="marker" value="18S"/>
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89 <param name="seqtype" value="forward"/>
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90 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
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91 <output name="outfile_report" ftype="tabular">
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92 <assert_contents>
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93 <has_text_matching expression="C.parvum"/>
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94 </assert_contents>
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95 </output>
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96 </test>
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97 <test>
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98 <param name="marker" value="gp60"/>
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99 <param name="seqtype" value="forward"/>
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100 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
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101 <output name="outfile_report" ftype="tabular" >
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102 <assert_contents>
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103 <has_text_matching expression="C.parvum"/>
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104 </assert_contents>
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105 </output>
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106 </test>
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107 </tests>
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108
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109
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110 <help>
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111
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112
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113 **Syntax**
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114
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115 CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers.
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116 For more information please visit https://github.com/phac-nml/CryptoGenotyper.
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117
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118 -----
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119
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120 **Input:**
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121
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122 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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123 Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification.
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124
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125
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126 **Output:**
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127
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128 FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample.
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129 </help>
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130 <citations>
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131 <citation type="bibtex">
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132 @misc{githubCryptoGenotyper,
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133 author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R},
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134 title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
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135 publisher = {GitHub},
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136 journal = {GitHub repository},
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137 url = {https://github.com/phac-nml/CryptoGenotyper}
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138 }</citation>
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139 </citations>
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140
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141 </tool>