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comparison prinseq.xml @ 3:02befcb391f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 475b8e0ad3472fb1daab4683530158813b4ef070
author iuc
date Mon, 15 May 2017 11:03:57 -0400
parents 74afc47f326c
children 654b3a274ed5
comparison
equal deleted inserted replaced
2:74afc47f326c 3:02befcb391f5
615 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option> 615 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
616 </param>--> 616 </param>-->
617 </inputs> 617 </inputs>
618 618
619 <outputs> 619 <outputs>
620 <data format="fastq" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq" 620 <data format_source="input_singles" name="good_sequence_file" from_work_dir="tmp/good_sequences.fastq"
621 label="${tool.name} on ${on_string}: Good sequences" > 621 label="${tool.name} on ${on_string}: Good sequences" >
622 <filter>seq_type['seq_type_opt'] == "single"</filter> 622 <filter>seq_type['seq_type_opt'] == "single"</filter>
623 </data> 623 </data>
624 <data format="fastq" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq" 624 <data format_source="input_singles" name="rejected_sequence_file" from_work_dir="tmp/rejected_sequences.fastq"
625 label="${tool.name} on ${on_string}: Rejected sequences" > 625 label="${tool.name} on ${on_string}: Rejected sequences" >
626 <filter>seq_type['seq_type_opt'] == "single"</filter> 626 <filter>seq_type['seq_type_opt'] == "single"</filter>
627 </data> 627 </data>
628 628
629 <data format="fastq" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq" 629 <data format_source="input_mate1" name="good_sequences_1_file" from_work_dir="tmp/good_sequences_1.fastq"
630 label="${tool.name} on ${on_string}: Good sequences for R1" > 630 label="${tool.name} on ${on_string}: Good sequences for R1" >
631 <filter>seq_type['seq_type_opt'] == "paired"</filter> 631 <filter>seq_type['seq_type_opt'] == "paired"</filter>
632 </data> 632 </data>
633 <data format="fastq" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq" 633 <data format_source="input_mate1" name="good_sequences_1_singletons_file" from_work_dir="tmp/good_sequences_1_singletons.fastq"
634 label="${tool.name} on ${on_string}: Good singleton sequences for R1" > 634 label="${tool.name} on ${on_string}: Good singleton sequences for R1" >
635 <filter>seq_type['seq_type_opt'] == "paired"</filter> 635 <filter>seq_type['seq_type_opt'] == "paired"</filter>
636 </data> 636 </data>
637 <data format="fastq" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq" 637 <data format_source="input_mate1" name="rejected_sequence_1_file" from_work_dir="tmp/rejected_sequences_1.fastq"
638 label="${tool.name} on ${on_string}: Rejected sequences for R1" > 638 label="${tool.name} on ${on_string}: Rejected sequences for R1" >
639 <filter>seq_type['seq_type_opt'] == "paired"</filter> 639 <filter>seq_type['seq_type_opt'] == "paired"</filter>
640 </data> 640 </data>
641 <data format="fastq" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq" 641 <data format_source="input_mate2" name="good_sequences_2_file" from_work_dir="tmp/good_sequences_2.fastq"
642 label="${tool.name} on ${on_string}: Good sequences for R2" > 642 label="${tool.name} on ${on_string}: Good sequences for R2" >
643 <filter>seq_type['seq_type_opt'] == "paired"</filter> 643 <filter>seq_type['seq_type_opt'] == "paired"</filter>
644 </data> 644 </data>
645 <data format="fastq" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq" 645 <data format_source="input_mate2" name="good_sequences_2_singletons_file" from_work_dir="tmp/good_sequences_2_singletons.fastq"
646 label="${tool.name} on ${on_string}: Good singleton sequences for R2" > 646 label="${tool.name} on ${on_string}: Good singleton sequences for R2" >
647 <filter>seq_type['seq_type_opt'] == "paired"</filter> 647 <filter>seq_type['seq_type_opt'] == "paired"</filter>
648 </data> 648 </data>
649 <data format="fastq" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq" 649 <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
650 label="${tool.name} on ${on_string}: Rejected sequences for R2" > 650 label="${tool.name} on ${on_string}: Rejected sequences for R2" >
651 <filter>seq_type['seq_type_opt'] == "paired"</filter> 651 <filter>seq_type['seq_type_opt'] == "paired"</filter>
652 </data> 652 </data>
653 653
654 <!--<data format="html" name="html_file" from_work_dir="stats_html.html" 654 <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
656 </outputs> 656 </outputs>
657 657
658 <tests> 658 <tests>
659 <test> 659 <test>
660 <param name='seq_type_opt' value="single"/> 660 <param name='seq_type_opt' value="single"/>
661 <param name="input_singles" value="prinseq_input_sequences.fastq"/> 661 <param name="input_singles" value="prinseq_input_sequences.fastq" ftype="fastqsanger"/>
662 <param name='apply_filter_treatments' value="true"/> 662 <param name='apply_filter_treatments' value="true"/>
663 <param name='apply_length_filter_treatments' value="true"/> 663 <param name='apply_length_filter_treatments' value="true"/>
664 <param name='apply_min_length_filter_treatments' value="true"/> 664 <param name='apply_min_length_filter_treatments' value="true"/>
665 <param name="min_length_filter_treatment_value" value="60"/> 665 <param name="min_length_filter_treatment_value" value="60"/>
666 <param name='apply_max_length_filter_treatments' value="false" /> 666 <param name='apply_max_length_filter_treatments' value="false" />
689 <param name="type_quality_trimming_treatments" value="min"/> 689 <param name="type_quality_trimming_treatments" value="min"/>
690 <param name="rule_quality_trimming_treatments" value="lt" /> 690 <param name="rule_quality_trimming_treatments" value="lt" />
691 <param name="window_quality_trimming_treatments" value="1"/> 691 <param name="window_quality_trimming_treatments" value="1"/>
692 <param name="step_quality_trimming_treatments" value="1"/> 692 <param name="step_quality_trimming_treatments" value="1"/>
693 693
694 <output name="good_sequence_file" file="prinseq_good_sequences.fastq"/> 694 <output name="good_sequence_file" file="prinseq_good_sequences.fastq" ftype="fastqsanger"/>
695 </test> 695 </test>
696 </tests> 696 </tests>
697 697
698 <help><![CDATA[ 698 <help><![CDATA[
699 **What it does** 699 **What it does**