Mercurial > repos > iuc > prinseq
comparison prinseq.xml @ 3:02befcb391f5 draft
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 |
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| 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** |