Mercurial > repos > nml > cryptogenotyper
comparison cryptogenotyper.xml @ 1:d4a96287909e draft default tip
"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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| 0:06afaa20dd23 | 1:d4a96287909e |
|---|---|
| 1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@"> | 1 <tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0"> |
| 2 <description> | 2 <description> |
| 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. | 3 classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data. |
| 4 </description> | 4 </description> |
| 5 <macros> | 5 <macros> |
| 6 <token name="@VERSION@">1.0</token> | 6 <token name="@VERSION@">1.0</token> |
| 7 </macros> | 7 </macros> |
| 8 <requirements> | 8 <requirements> |
| 12 <command detect_errors="exit_code"> | 12 <command detect_errors="exit_code"> |
| 13 <![CDATA[ | 13 <![CDATA[ |
| 14 | 14 |
| 15 #set $ref_file='' | 15 #set $ref_file='' |
| 16 | 16 |
| 17 #if $reference.ref == "no" | 17 #if $db |
| 18 ln -s "${reference.db}" "${reference.db.name}" && | 18 ln -s '${db}' '${db.name}' && |
| 19 #set $ref_file = $reference.db.name | 19 #set $ref_file = $db.name |
| 20 #end if | 20 #end if |
| 21 | 21 |
| 22 #if $primers["seqtype"] == "contig" | 22 #if $primers['seqtype'] == 'contig' |
| 23 ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" && | 23 ln -s '${$primers.abi_input['forward']}' '${primers.abi_input.name}_forward.ab1' && |
| 24 ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" && | 24 ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' && |
| 25 cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse" | 25 cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse' |
| 26 #if $reference.ref == "no" | 26 #if $db |
| 27 --databasefile $ref_file | 27 --databasefile $ref_file |
| 28 #end if | 28 #end if |
| 29 #else | 29 #else |
| 30 ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" && | 30 ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' && |
| 31 cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r "" | 31 cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype' |
| 32 #if $reference.ref == "no" | 32 #if $db |
| 33 --databasefile $ref_file | 33 --databasefile $ref_file |
| 34 #end if | 34 #end if |
| 35 #end if | 35 #end if |
| 36 #if $outputheader == "no" | 36 $outputheader |
| 37 --noheaderline | 37 -o 'result' |
| 38 #end if | |
| 39 -o "result"; | |
| 40 ]]> | 38 ]]> |
| 41 </command> | 39 </command> |
| 42 <inputs> | 40 <inputs> |
| 43 <param name="marker" type="select" label="Marker"> | 41 <param name="marker" type="select" label="Marker"> |
| 44 <option value="18S">SSU rRNA</option> | 42 <option value="18S">SSU rRNA</option> |
| 45 <option value="gp60">gp60</option> | 43 <option value="gp60">gp60</option> |
| 46 </param> | 44 </param> |
| 47 <conditional name="reference"> | 45 <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/> |
| 48 <param name="ref" type="select" label="Use default reference file?"> | |
| 49 <option value="yes">Yes</option> | |
| 50 <option value="no">No</option> | |
| 51 </param> | |
| 52 <when value="yes"> | |
| 53 </when> | |
| 54 <when value="no"> | |
| 55 <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/> | |
| 56 </when> | |
| 57 </conditional> | |
| 58 <conditional name="primers"> | 46 <conditional name="primers"> |
| 59 <param name="seqtype" type="select" label="Type of Sequences"> | 47 <param name="seqtype" type="select" label="Type of Sequences"> |
| 60 <option value="forward">Forward Only</option> | 48 <option value="forward">Forward Only</option> |
| 61 <option value="reverse">Reverse Only</option> | 49 <option value="reverse">Reverse Only</option> |
| 62 <option selected="true" value="contig">Contig</option> | 50 <option selected="true" value="contig">Contig</option> |
| 63 </param> | 51 </param> |
| 64 <when value="contig"> | 52 <when value="contig"> |
| 65 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/> | 53 <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/> |
| 66 </when> | 54 </when> |
| 67 <when value="forward"> | 55 <when value="forward"> |
| 68 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/> | 56 <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/> |
| 69 </when> | 57 </when> |
| 70 <when value="reverse"> | 58 <when value="reverse"> |
| 71 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/> | 59 <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/> |
| 72 </when> | 60 </when> |
| 73 </conditional> | 61 </conditional> |
| 74 <param name="outputheader" type="select" value="yes" label="Output header line in the report?"> | 62 <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?"> |
| 75 <option value="yes">Yes</option> | |
| 76 <option value="no">No</option> | |
| 77 </param> | 63 </param> |
| 78 | 64 |
| 79 | 65 |
| 80 </inputs> | 66 </inputs> |
| 81 <outputs> | 67 <outputs> |
| 82 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/> | 68 <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/> |
| 83 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/> | 69 <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/> |
| 84 </outputs> | 70 </outputs> |
| 85 | 71 |
| 86 <tests> | 72 <tests> |
| 87 <test> | 73 <test expect_num_outputs="2"> |
| 88 <param name="marker" value="18S"/> | 74 <param name="marker" value="18S"/> |
| 89 <param name="seqtype" value="forward"/> | 75 <param name="seqtype" value="forward"/> |
| 90 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> | 76 <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> |
| 91 <output name="outfile_report" ftype="tabular"> | 77 <output name="outfile_report" ftype="tabular"> |
| 92 <assert_contents> | 78 <assert_contents> |
| 93 <has_text_matching expression="C.parvum"/> | 79 <has_text_matching expression="C.parvum"/> |
| 94 </assert_contents> | 80 </assert_contents> |
| 95 </output> | 81 </output> |
| 96 </test> | 82 </test> |
| 97 <test> | 83 <test expect_num_outputs="2"> |
| 98 <param name="marker" value="gp60"/> | 84 <param name="marker" value="gp60"/> |
| 99 <param name="seqtype" value="forward"/> | 85 <param name="seqtype" value="forward"/> |
| 100 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/> | 86 <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/> |
| 101 <output name="outfile_report" ftype="tabular" > | 87 <output name="outfile_report" ftype="tabular" > |
| 102 <assert_contents> | 88 <assert_contents> |