Mercurial > repos > devteam > fastq_paired_end_interlacer
comparison fastq_paired_end_interlacer.xml @ 1:ec6ddf449651 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit a5821127c24ed3bf1e9d5ba4fb8b9f3eceb0f3f3
author | devteam |
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date | Sat, 19 Mar 2016 09:41:17 -0400 |
parents | b89bdf6acb6c |
children | effda79f510c |
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0:b89bdf6acb6c | 1:ec6ddf449651 |
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1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.1"> | 1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2"> |
2 <description>on paired end reads</description> | 2 <description>on paired end reads</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | 4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
5 </requirements> | 5 </requirements> |
6 <command interpreter="python">fastq_paired_end_interlacer.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$outfile_pairs' '$outfile_singles'</command> | 6 <command> |
7 python $__tool_directory__/fastq_paired_end_interlacer.py | |
8 #if $reads.reads_selector == 'paired' | |
9 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]} | |
10 #else | |
11 '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]} | |
12 #end if | |
13 '$outfile_pairs' '$outfile_singles' | |
14 </command> | |
7 <inputs> | 15 <inputs> |
8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" /> | 16 <conditional name="reads"> |
9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" /> | 17 <param name="reads_selector" type="select" label="Type of paired-end datasets"> |
18 <option value="paired">2 separate datasets</option> | |
19 <option value="paired_collection">1 paired dataset collection</option> | |
20 </param> | |
21 <when value="paired"> | |
22 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" /> | |
23 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" /> | |
24 </when> | |
25 <when value="paired_collection"> | |
26 <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger" label="Paired-end reads collection" /> | |
27 </when> | |
28 </conditional> | |
10 </inputs> | 29 </inputs> |
11 <outputs> | 30 <outputs> |
12 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger --> | 31 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger --> |
13 <!-- $input1_file.id = ID , e.g. 10 --> | 32 <!-- $input1_file.id = ID , e.g. 10 --> |
14 <!-- $input1_file.hid = history ID, e.g. 5 --> | 33 <!-- $input1_file.hid = history ID, e.g. 5 --> |
15 <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from data ${input1_file.hid} and data ${input2_file.hid}"/> | 34 <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from ${on_string}"/> |
16 <data name="outfile_singles" format="input" label="FASTQ interlacer singles from data ${input1_file.hid} and data ${input2_file.hid}"/> | 35 <data name="outfile_singles" format="input" label="FASTQ interlacer singles from ${on_string}"/> |
17 </outputs> | 36 </outputs> |
18 <tests> | 37 <tests> |
19 <test> | 38 <test> |
39 <param name="reads_selector" value="paired" /> | |
20 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> | 40 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> |
21 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> | 41 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> |
22 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" /> | 42 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> |
23 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" /> | 43 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> |
24 </test> | 44 </test> |
25 <test> | 45 <test> |
46 <param name="reads_selector" value="paired" /> | |
26 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> | 47 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" /> |
27 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> | 48 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" /> |
28 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" /> | 49 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" /> |
29 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" /> | 50 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" /> |
51 </test> | |
52 <test> | |
53 <param name="reads_selector" value="paired_collection" /> | |
54 <param name="reads_coll"> | |
55 <collection type="paired"> | |
56 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" /> | |
57 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" /> | |
58 </collection> | |
59 </param> | |
60 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" /> | |
61 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" /> | |
30 </test> | 62 </test> |
31 </tests> | 63 </tests> |
32 <help> | 64 <help> |
33 **What it does** | 65 **What it does** |
34 | 66 |
68 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT | 100 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT |
69 +1539:931/2 | 101 +1539:931/2 |
70 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB | 102 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB |
71 | 103 |
72 A multiple-fastq file containing reads that have no mate is also produced. | 104 A multiple-fastq file containing reads that have no mate is also produced. |
73 | |
74 </help> | 105 </help> |
106 <citations> | |
107 <citation doi="10.1093/bioinformatics/btq281" /> | |
108 </citations> | |
75 </tool> | 109 </tool> |