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comparison macros.xml @ 14:83b3744d6ced draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 099f08cce5c93f4ed22bc8b02296fd4b5d357390
author iuc
date Mon, 03 Mar 2025 11:05:55 +0000
parents 72c85da3f6a8
children 3da6bde1f252
comparison
equal deleted inserted replaced
13:72c85da3f6a8 14:83b3744d6ced
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.15.4</token> 2 <token name="@TOOL_VERSION@">3.15.5</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">3</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
7 <requirement type="package" version="3.0">zip</requirement> 7 <requirement type="package" version="3.0">zip</requirement>
8 <yield/> 8 <yield/>
146 <!-- COMMANDS --> 146 <!-- COMMANDS -->
147 147
148 <token name="@RESOURCES@"><![CDATA[ 148 <token name="@RESOURCES@"><![CDATA[
149 -t \${GALAXY_SLOTS:-4} 149 -t \${GALAXY_SLOTS:-4}
150 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024)) 150 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024))
151 --tmp-dir \${TMPDIR}
151 ]]></token> 152 ]]></token>
152 153
153 <token name="@INPUT_READS_MAIN@"><![CDATA[ 154 <token name="@INPUT_READS_MAIN@"><![CDATA[
154 #if $singlePaired.sPaired == "single" 155 #if $singlePaired.sPaired == "single"
155 #for $read in $file_paths1 156 #for $read in $file_paths1
382 383
383 <!-- POSTPROCESSING --> 384 <!-- POSTPROCESSING -->
384 385
385 <token name="@STATS@"><![CDATA[ 386 <token name="@STATS@"><![CDATA[
386 #if 'cs' in $optional_output 387 #if 'cs' in $optional_output
387 && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.' 388 && (test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.')
388 #end if 389 #end if
389 #if 'ss' in $optional_output 390 #if 'ss' in $optional_output
390 && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.' 391 && (test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.')
391 #end if 392 #end if
392 ]]></token> 393 ]]></token>
393 394
394 <token name="@CORRECTED@"><![CDATA[ 395 <token name="@CORRECTED@"><![CDATA[
395 #if 'corrected' in $optional_output 396 #if 'corrected' in $optional_output
396 && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.' 397 && (test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.')
397 #end if 398 #end if
398 ]]></token> 399 ]]></token>
399 400
400 <!-- 401 <!--
401 input 402 input
502 <option value="false" selected="true">Disabled</option> 503 <option value="false" selected="true">Disabled</option>
503 <option value="true">Enabled</option> 504 <option value="true">Enabled</option>
504 </param> 505 </param>
505 <when value="true"> 506 <when value="true">
506 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/> 507 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
507 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
508 <option value="true" selected="true">True</option>
509 <option value="false">False</option>
510 </param>
511 </when> 508 </when>
512 <when value="false"/> 509 <when value="false"/>
513 </conditional> 510 </conditional>
514 </xml> 511 </xml>
515 512