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annotate cryptogenotyper.xml @ 0:c64e19bda2a6 draft default tip

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planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
author nml
date Fri, 12 Sep 2025 18:50:28 +0000
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0
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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2 <description>
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3 classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data.
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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4 </description>
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5 <macros>
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6 <token name="@VERSION@">1.5.0</token>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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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>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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15 #set $ref_file=''
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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16
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17 #if $db
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18 ln -sf '${db}' '${db.name}' &&
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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19 #set $ref_file = $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 #set $forward_name=$primers.input.forward.name.rsplit('.', 1)[0]
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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24 #set $reverse_name=$primers.input.reverse.name.rsplit('.', 1)[0]
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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25 ln -sf '${$primers.input['forward']}' '${forward_name}_forward.${primers.input.forward.ext}' &&
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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26 ln -sf '${$primers.input['reverse']}' '${reverse_name}_reverse.${primers.input.reverse.ext}' &&
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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27 cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse'
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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28 #if $db
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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29 --databasefile $ref_file
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30 #end if
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31 #else
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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32 #set $filename_no_ext=$primers.input.name.rsplit('.', 1)[0]
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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33 ln -sf '${primers.input}' '${filename_no_ext}.${primers.input.ext}' &&
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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34 cryptogenotyper -i './${primers.input.name}' -m '$marker' -t '$primers.seqtype'
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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35 #if $db
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36 --databasefile $ref_file
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37 #end if
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38 #end if
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39 $outputheader
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40 -o 'result'
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41 ]]>
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42 </command>
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43 <inputs>
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44 <param name="marker" type="select" label="Marker">
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45 <option value="18S">SSU rRNA (18S)</option>
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46 <option value="gp60">gp60</option>
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47 </param>
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48 <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/>
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49 <conditional name="primers">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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50 <param name="seqtype" type="select" label="Type of Sequences">
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51 <option value="forward" selected="true">Forward Only</option>
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52 <option value="reverse">Reverse Only</option>
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53 <option value="contig">Contig</option>
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54 </param>
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55 <when value="contig">
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56 <param name="input" type="data_collection" collection_type="paired" format="ab1,fasta" label="Paired Sequencing File(s)"/>
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57 </when>
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58 <when value="forward">
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59 <param name="input" type="data" format="ab1,fasta" label="Forward Sequencing File(s)"/>
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60 </when>
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61 <when value="reverse">
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62 <param name="input" type="data" format="ab1,fasta" label="Reverse Sequencing File(s)"/>
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63 </when>
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64 </conditional>
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65 <param name="show_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output run log?"></param>
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66 <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?">
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67 </param>
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68
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69
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70 </inputs>
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71 <outputs>
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72 <!-- For single files (forward/reverse mode) -->
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73 <data name="outfile_single" format="fasta" from_work_dir="result_cryptogenotyper_report.fa"
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74 label="${tool.name} ${marker} extracted fasta from ${primers.input.name.split('.')[0]}">
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75 <filter>primers['seqtype'] != 'contig'</filter>
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76 </data>
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77 <!-- For collections (contig mode) -->
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78 <data name="outfile_collection" format="fasta" from_work_dir="result_cryptogenotyper_report.fa"
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79 label="${tool.name} ${marker} extracted fastas">
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80 <filter>primers['seqtype'] == 'contig'</filter>
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81 </data>
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82
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83 <!-- For single files (forward/reverse mode) -->
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84 <data name="outfile_report_single" format="tabular" from_work_dir="result_cryptogenotyper_report.txt"
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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85 label="${tool.name} ${marker} REPORT on ${primers.input.name.split('.')[0]}">
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86 <filter>primers['seqtype'] != 'contig'</filter>
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87 </data>
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88 <!-- For collections (contig mode) -->
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89 <data name="outfile_report_collection" format="tabular" from_work_dir="result_cryptogenotyper_report.txt"
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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90 label="${tool.name} ${marker} REPORTS">
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91 <filter>primers['seqtype'] == 'contig'</filter>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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92 </data>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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93
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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94 <!-- For single files (forward/reverse mode) -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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95 <data name="outfile_log_single" format="txt" from_work_dir="cryptogenotyper.log"
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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96 label="${tool.name} Run ${marker} log on ${primers.input.name.split('.')[0]}">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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97 <filter>show_log and primers['seqtype'] != 'contig'</filter>
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98 </data>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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99 <!-- For collections (contig mode) -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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100 <data name="outfile_log_collection" format="txt" from_work_dir="cryptogenotyper.log"
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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101 label="${tool.name} ${marker} logs">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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102 <filter>show_log and primers['seqtype'] == 'contig'</filter>
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103 </data>
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104 </outputs>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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105
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106 <tests>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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107 <!--TEST 1-->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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108 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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109 <param name="marker" value="18S"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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110 <conditional name="primers">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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111 <param name="seqtype" value="forward"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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112 <param name="input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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113 </conditional>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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114 <output name="outfile_report_single" ftype="tabular">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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115 <assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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116 <has_text_matching expression="C.parvum"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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117 </assert_contents>
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118 </output>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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119 </test>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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120 <!--TEST 2 -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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121 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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122 <param name="marker" value="gp60"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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123 <conditional name="primers">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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124 <param name="seqtype" value="forward"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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125 <param name="input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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126 </conditional>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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127 <output name="outfile_report_single" ftype="tabular" >
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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128 <assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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129 <has_text_matching expression="C.parvum"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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130 </assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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131 </output>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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132 </test>
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133 <!--TEST 3:Paired gp60 contig test -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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134 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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135 <param name="marker" value="gp60"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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136 <param name="primers|seqtype" value="contig"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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137 <param name="primers|input">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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138 <collection type="paired">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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139 <element name="forward" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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140 <element name="reverse" value="P17705_gp60-Crypt14-1R-20170927_gp60R_H07_049.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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141 </collection>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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142 </param>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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143 <output name="outfile_report_collection" ftype="tabular">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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144 <assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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145 <has_text_matching expression="C.parvum"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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146 <has_text_matching expression="IIaA15G2R1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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147 </assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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148 </output>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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149 </test>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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150 <!--TEST 4:Paired 18S contig test -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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151 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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152 <param name="marker" value="18S"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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153 <param name="primers|seqtype" value="contig"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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154 <param name="primers|input">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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155 <collection type="paired">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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156 <element name="forward" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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157 <element name="reverse" value="P17705_Crypto16-2R-20170927_SSUR_H12_082.ab1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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158 </collection>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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159 </param>
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160 <output name="outfile_report_collection" ftype="tabular">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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161 <assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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162 <has_text_matching expression="C.parvum"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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163 <has_text_matching expression="Check for C. parvum TGA paralogs"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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164 </assert_contents>
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165 </output>
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166 </test>
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167
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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168
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169 <!--TEST 5: 18S multi-fasta forward -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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170 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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171 <param name="marker" value="18S"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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172 <param name="primers|seqtype" value="forward"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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173 <param name="primers|input" value="test_illumina_18S_F.fasta"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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174 <output name="outfile_report_single" ftype="tabular">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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175 <assert_contents>
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176 <has_n_lines n="5"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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177 <has_text_matching expression="C.hominis"/>
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178 <has_text_matching expression="forward"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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179 </assert_contents>
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180 </output>
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181 </test>
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182
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183 <!--TEST 6: 18S multi-fasta reverse -->
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184 <test expect_num_outputs="2">
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185 <param name="marker" value="18S"/>
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186 <param name="primers|seqtype" value="reverse"/>
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187 <param name="primers|input" value="test_illumina_18S_R.fasta"/>
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188 <output name="outfile_report_single" ftype="tabular">
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189 <assert_contents>
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190 <has_n_lines n="5"/>
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191 <has_text_matching expression="C.hominis"/>
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192 <has_text_matching expression="reverse"/>
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193 </assert_contents>
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194 </output>
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195 </test>
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196
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197 <!--TEST 7: 18S multi-fasta contig -->
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198 <test expect_num_outputs="2">
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199 <param name="marker" value="18S"/>
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200 <param name="primers|seqtype" value="contig"/>
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201 <param name="primers|input">
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202 <collection type="paired">
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203 <element name="forward" value="test_illumina_18S_F.fasta"/>
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204 <element name="reverse" value="test_illumina_18S_R.fasta"/>
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205 </collection>
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206 </param>
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207 <output name="outfile_report_collection" ftype="tabular">
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208 <assert_contents>
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209 <has_text_matching expression="C.hominis"/>
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210 <has_text_matching expression="contig"/>
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211 </assert_contents>
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212 </output>
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213 </test>
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214
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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215 <!--TEST 8: gp60 multi-fasta forward -->
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216 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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217 <param name="marker" value="gp60"/>
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218 <param name="primers|seqtype" value="forward"/>
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219 <param name="primers|input" value="test_illumina_gp60_F1.fasta"/>
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220 <output name="outfile_report_single" ftype="tabular">
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221 <assert_contents>
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222 <has_n_lines n="3"/>
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223 <has_text_matching expression="C.parvum"/>
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224 <has_text_matching expression="forward"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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225 <has_text_matching expression="IIaA16G3R1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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226 <has_text_matching expression="IIaA15G2R2"/>
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227
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228 </assert_contents>
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229 </output>
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230 </test>
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231
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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232 <!--TEST 9: gp60 multi-fasta reverse -->
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233 <test expect_num_outputs="2">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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234 <param name="marker" value="gp60"/>
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235 <param name="primers|seqtype" value="reverse"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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236 <param name="primers|input" value="test_illumina_gp60_R1.fasta"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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237 <output name="outfile_report_single" ftype="tabular">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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238 <assert_contents>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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239 <has_n_lines n="3"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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240 <has_text_matching expression="C.parvum"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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241 <has_text_matching expression="reverse"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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242 <has_text_matching expression="IIaA3R1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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243 <has_text_matching expression="IIaA3R1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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244 </assert_contents>
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245 </output>
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246 </test>
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247
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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248
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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249
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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250 <!--TEST 10: gp60 multi-fasta reverse -->
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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251 <test expect_num_outputs="3">
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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252 <param name="marker" value="gp60"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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253 <param name="primers|seqtype" value="contig"/>
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254 <param name="show_log" value="true"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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255 <param name="primers|input">
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256 <collection type="paired">
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257 <element name="forward" value="test_illumina_gp60_F1.fasta"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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258 <element name="reverse" value="test_illumina_gp60_R1.fasta"/>
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259 </collection>
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260 </param>
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261 <output name="outfile_report_collection" ftype="tabular">
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262 <assert_contents>
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263 <has_text_matching expression="C.parvum"/>
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264 <has_text_matching expression="contig"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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265 <has_text_matching expression="IIaA16G3R1"/>
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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266 <has_text_matching expression="IIaA15G2R2"/>
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267 </assert_contents>
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268 </output>
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269 </test>
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270
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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271
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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272
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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273
c64e19bda2a6 planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit fdca1f95a5d09edf00bddd42286b68fcb20fa981
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274
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275 </tests>
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276
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277
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278 <help>
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279
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280
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281 **Syntax**
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282
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283 CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA (18S) and gp60 markers.
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284
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285 **❗ Important:** To process **multiple input files** and generate **a single** combined report, please import and use the workflows available `here`_.
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286
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287 .. _here: https://github.com/phac-nml/CryptoGenotyper/tree/main/CryptoGenotyper/GalaxyWorkflows
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288
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289
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290 For a tutorial on how to use CryptoGenotyper, please refer to the `official tutorial`_.
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291
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292 For more information, please visit https://github.com/phac-nml/CryptoGenotyper.
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293
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294 .. _official tutorial: https://github.com/phac-nml/CryptoGenotyper/blob/docs/docs/CryptoGenotyperTutorial-CrownCopyright.pdf
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295
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296 -----
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297
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298 **Input:**
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299
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300 AB1 or FASTA file(s) representing Cryptosporidium's SSU rRNA (18S) or gp60 locus can be provided as single-end reads (either forward or reverse only) or as paired-end reads in contig mode (both a forward and a reverse read for each sample).
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301
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302 Optional: A custom reference database of SSU rRNA or gp60 locus in .fasta file format, to be used during the homology search for *Cryptosporidium* classification.
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303
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304
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305 **Output:**
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306
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307 A tabular report and a FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample along with other relevant details.
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308 The gp60 subtyping is based on the `Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`_.
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309
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310 .. _`Deciphering a cryptic minefield: a guide to Cryptosporidium gp60 subtyping publication`: https://doi.org/10.1016/j.crpvbd.2025.100257
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311
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312 </help>
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313 <citations>
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314 <citation type="bibtex">
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315 @ARTICLE{githubCryptoGenotyper,
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316 author = {Yanta, Christine A. and Bessonov, Kyrylo and Robinson, Guy and Troell, Karin and Guy, Rebecca A.},
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317 title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification},
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318 journal = {Food and waterborne parasitology},
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319 year = {2021},
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320 volume = {23},
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321 url = {https://doi.org/10.1016/j.fawpar.2021.e00115}
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322 }</citation>
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323 <citation type="bibtex">
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324 @ARTICLE{RobinsonGp60,
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325 author = {Robinson, Gillian and Chalmers, Rachel M. and Elwin, Kirsty and Guy, Richard A. and Bessonov, Konstantin and Troell, Kristina and Xiao, Lihua},
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326 title = {Deciphering a cryptic minefield: A guide to Cryptosporidium gp60 subtyping},
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327 journal = {Current Research in Parasitology and Vector-Borne Diseases},
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328 year = {2025},
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329 volume = {7},
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330 url = {https://doi.org/10.1016/j.crpvbd.2025.100257}
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331 }
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332 }</citation>
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333 </citations>
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334
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335 </tool>