Mercurial > repos > iuc > colibread_kissplice
diff macros.xml @ 0:4acdd256cc12 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author | iuc |
---|---|
date | Fri, 20 Oct 2017 03:14:17 -0400 |
parents | |
children | d5b4404c4788 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Oct 20 03:14:17 2017 -0400 @@ -0,0 +1,42 @@ +<macros> + <token name="@discosnp_single_reads@"><![CDATA[ + #for $input in $input_type_options.list_reads + #set $filename = str($input) + "." + $input.ext + ln -sf '${input}' '${filename}' && + echo '${filename}' >> input.lst && + #end for + ]]></token> + <token name="@discosnp_paired_reads@"><![CDATA[ + #for $i, $paired in enumerate( $input_type_options.list_paired_reads ) + + #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext + ln -sf '${paired.forward}' '${filenameFWD}' && + + #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext + ln -sf '${paired.reverse}' '${filenameREV}' && + + echo '${filenameFWD}' > "paired_${i}.lst" && + echo '${filenameREV}' >> "paired_${i}.lst" && + echo "paired_${i}.lst" >> input.lst && + + #end for + ]]></token> + <token name="@lordec_inputs@"><![CDATA[ + -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }" + -i '${program_type_choice.i}' + -k ${program_type_choice.k} + -s ${program_type_choice.s} + ]]></token> + <xml name="lordec_inputs"> + <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" /> + <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" /> + <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/> + <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" /> + </xml> + <xml name="citations"> + <citations> + <yield/> + <citation type="doi">10.1186/s13742-015-0105-2</citation> + </citations> + </xml> +</macros>