Mercurial > repos > nml > cryptogenotyper
changeset 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 | |
files | cryptogenotyper.xml |
diffstat | 1 files changed, 22 insertions(+), 36 deletions(-) [+] |
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--- a/cryptogenotyper.xml Fri Oct 16 02:23:24 2020 +0000 +++ b/cryptogenotyper.xml Fri Oct 16 22:32:56 2020 +0000 @@ -1,6 +1,6 @@ -<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@"> +<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@+galaxy0"> <description> - 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. + classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data. </description> <macros> <token name="@VERSION@">1.0</token> @@ -14,29 +14,27 @@ #set $ref_file='' - #if $reference.ref == "no" - ln -s "${reference.db}" "${reference.db.name}" && - #set $ref_file = $reference.db.name + #if $db + ln -s '${db}' '${db.name}' && + #set $ref_file = $db.name #end if - #if $primers["seqtype"] == "contig" - ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" && - ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" && - cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse" - #if $reference.ref == "no" + #if $primers['seqtype'] == 'contig' + ln -s '${$primers.abi_input['forward']}' '${primers.abi_input.name}_forward.ab1' && + ln -s '${$primers.abi_input['reverse']}' '${primers.abi_input.name}_reverse.ab1' && + cryptogenotyper -i '.' -m '$marker' -t '$primers.seqtype' -f 'forward' -r 'reverse' + #if $db --databasefile $ref_file #end if #else - ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" && - cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r "" - #if $reference.ref == "no" + ln -s '${primers.abi_input}' '${primers.abi_input.element_identifier}' && + cryptogenotyper -i './${primers.abi_input.element_identifier}' -m '$marker' -t '$primers.seqtype' + #if $db --databasefile $ref_file #end if #end if - #if $outputheader == "no" - --noheaderline - #end if - -o "result"; + $outputheader + -o 'result' ]]> </command> <inputs> @@ -44,17 +42,7 @@ <option value="18S">SSU rRNA</option> <option value="gp60">gp60</option> </param> - <conditional name="reference"> - <param name="ref" type="select" label="Use default reference file?"> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> - <when value="yes"> - </when> - <when value="no"> - <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/> - </when> - </conditional> + <param name="db" type="data" optional="true" format="fasta" label="Reference Database File (optional):"/> <conditional name="primers"> <param name="seqtype" type="select" label="Type of Sequences"> <option value="forward">Forward Only</option> @@ -62,18 +50,16 @@ <option selected="true" value="contig">Contig</option> </param> <when value="contig"> - <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/> + <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)"/> </when> <when value="forward"> - <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/> + <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)"/> </when> <when value="reverse"> - <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/> + <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)"/> </when> </conditional> - <param name="outputheader" type="select" value="yes" label="Output header line in the report?"> - <option value="yes">Yes</option> - <option value="no">No</option> + <param name="outputheader" type="boolean" truevalue="" falsevalue="--noheaderline" checked="true" label="Output header line in the report?"> </param> @@ -84,7 +70,7 @@ </outputs> <tests> - <test> + <test expect_num_outputs="2"> <param name="marker" value="18S"/> <param name="seqtype" value="forward"/> <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> @@ -94,7 +80,7 @@ </assert_contents> </output> </test> - <test> + <test expect_num_outputs="2"> <param name="marker" value="gp60"/> <param name="seqtype" value="forward"/> <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/>