Mercurial > repos > lparsons > cutadapt
comparison cutadapt.xml @ 29:48f587c13075 draft
"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 |
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| 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" /> |