Mercurial > repos > lparsons > cutadapt

comparison cutadapt.xml @ 29:48f587c13075 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit dea830212266690dbd20448f9a89ea7bfeee4a26"
author iuc
date Thu, 10 Feb 2022 12:13:05 +0000
parents c053d4cad713
children c5e2e5902201
comparison
equal deleted inserted replaced
28:c053d4cad713 29:48f587c13075
91 --output='$out1' 91 --output='$out1'
92 #end if 92 #end if
93 #else: 93 #else:
94 @read1_options@ 94 @read1_options@
95 @read2_options@ 95 @read2_options@
96 #if $library.type == "paired" 96 --output='$out1'
97 --output='$out1' 97 --paired-output='$out2'
98 --paired-output='$out2'
99 #else
100 --output='$out_pairs.forward'
101 --paired-output='$out_pairs.reverse'
102 #end if
103 #end if 98 #end if
104 99
105 --error-rate=$adapter_options.error_rate 100 --error-rate=$adapter_options.error_rate
106 --times=$adapter_options.times 101 --times=$adapter_options.times
107 --overlap=$adapter_options.overlap 102 --overlap=$adapter_options.overlap
335 <expand macro="inherit_format_2" /> 330 <expand macro="inherit_format_2" />
336 </data> 331 </data>
337 332
338 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads"> 333 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
339 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter> 334 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
335 <data name="forward" from_work_dir="out1.fq*" />
336 <data name="reverse" from_work_dir="out2.fq*" />
340 </collection> 337 </collection>
341 338
342 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> 339 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
343 <filter>output_selector and 'report' in output_selector</filter> 340 <filter>output_selector and 'report' in output_selector</filter>
344 </data> 341 </data>
476 <param name="adapter_source_list2" value="user"/> 473 <param name="adapter_source_list2" value="user"/>
477 <param name="adapter2" value="AGATCGGAAGAGC"/> 474 <param name="adapter2" value="AGATCGGAAGAGC"/>
478 </conditional> 475 </conditional>
479 </repeat> 476 </repeat>
480 </section> 477 </section>
481 <output_collection name="out_pairs" type="paired"> 478 <output_collection name="out_pairs" type="paired" count="2">
482 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" /> 479 <element name="forward" decompress="true" file="cutadapt_out1.fq.gz" ftype="fastq.gz">
483 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" /> 480 <assert_contents>
481 <has_size value="12000" delta="2000" />
482 </assert_contents>
483 </element>
484 <element name="reverse" decompress="true" file="cutadapt_out2.fq.gz" ftype="fastq.gz">
485 <assert_contents>
486 <has_size value="12000" delta="2000" />
487 </assert_contents>
488 </element>
484 </output_collection> 489 </output_collection>
485 </test> 490 </test>
486 <!-- Ensure built-in adapters work --> 491 <!-- Ensure built-in adapters work -->
487 <test expect_num_outputs="1"> 492 <test expect_num_outputs="1">
488 <param name="type" value="single" /> 493 <param name="type" value="single" />