Mercurial > repos > iuc > stacks_procrad
diff stacks_procrad.xml @ 8:bec1f08cdfcc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
| author | iuc |
|---|---|
| date | Thu, 27 Apr 2017 04:19:34 -0400 |
| parents | 2837e6ae4e18 |
| children | 57910d476be9 |
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--- a/stacks_procrad.xml Fri Apr 07 11:49:00 2017 -0400 +++ b/stacks_procrad.xml Thu Apr 27 04:19:34 2017 -0400 @@ -7,29 +7,29 @@ <expand macro="stdio"/> <command><![CDATA[ - #if $input_type.options_type_selector == "single": + #if $input_type.options_type_selector == "single" - #if $input_type.input_single.is_of_type('fastqsanger'): + #if $input_type.input_single.is_of_type('fastqsanger') #set $ext = ".fq" #set inputype = "fastq" - #else: + #else #set $ext = ".fq.gz" #set inputype = "gzfastq" #end if - ln -s "$input_type.input_single" R1$ext && + ln -s '$input_type.input_single' R1$ext && #else - #if $input_type.inputs_paired1.is_of_type('fastqsanger'): + #if $input_type.inputs_paired1.is_of_type('fastqsanger') #set $ext = ".fq" #set inputype = "fastq" - #else: + #else #set $ext = ".fq.gz" #set inputype = "gzfastq" #end if - ln -s "$input_type.inputs_paired1" R1$ext && - ln -s "$input_type.inputs_paired2" R2$ext && + ln -s '$input_type.inputs_paired1' R1$ext && + ln -s '$input_type.inputs_paired2' R2$ext && #end if mkdir stacks_outputs @@ -38,31 +38,33 @@ process_radtags - #if $input_type.options_type_selector == "single": + #if $input_type.options_type_selector == "single" -f R1$ext - #else: + #else -1 R1$ext -2 R2$ext #end if -i $inputype - -b "$barcode" + -b '$barcode' $input_type.barcode_encoding - #if str( $options_enzyme.options_enzyme_selector ) == "1": + #if str( $options_enzyme.options_enzyme_selector ) == "1" -e $options_enzyme.enzyme - #else: + #else --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2 #end if - -y $outype + #if str( $outype ) != "auto" + -y $outype + #end if $capture $options_advanced.retain_header - #if str($options_advanced.truncate): + #if str($options_advanced.truncate) -t $options_advanced.truncate #end if @@ -85,7 +87,7 @@ <option value="paired">Paired-end files</option> </param> <when value="single"> - <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" /> + <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> <param name="barcode_encoding" type="select" label="Barcode location"> <option value="--inline_null" selected="True">Barcode is inline with sequence</option> @@ -93,8 +95,8 @@ </param> </when> <when value="paired"> - <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> - <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> + <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> + <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> <param name="barcode_encoding" type="select" label="Barcode location"> <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option> @@ -141,10 +143,11 @@ <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> </section> - <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy --> - <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" > - <option value="fastq" selected="True">fastq</option> + <param name="outype" argument="-y" type="select" label="Output format" > + <option value="auto" selected="True">Same as input</option> + <option value="fastq">fastq</option> <option value="fasta">fasta</option> + <option value="gzfastq">gzipped fastq</option> </param> </inputs> @@ -153,16 +156,19 @@ <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> <filter>input_type['options_type_selector'] == "paired"</filter> <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> <filter>capture is True</filter> <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped --> <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" /> </collection> </outputs> @@ -189,6 +195,23 @@ </output_collection> </test> <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <param name="outype" value="gzfastq"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> + </output_collection> + </test> + <test> <param name="options_type_selector" value="paired"/> <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> @@ -262,6 +285,43 @@ </element> </output_collection> </test> + <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1"> + <assert_contents> + <has_text text="lane1_fakedata0_11" /> + </assert_contents> + </element> + </output_collection> + </test> + <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <param name="outype" value="gzfastq"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> + </output_collection> + </test> </tests>