Mercurial > repos > brenninc > tagdust_2_31
comparison paired.xml @ 0:40c86e14b674 draft
Uploaded first version of tagdust
author | brenninc |
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date | Mon, 09 May 2016 04:08:01 -0400 |
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-1:000000000000 | 0:40c86e14b674 |
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1 <tool id="tagdust_paired_runner_2_31" name="Tagdust paired end runner" version="0.2"> | |
2 <description>Runs tagdust in paired end mode</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"></expand> | |
7 <expand macro="stdio"></expand> | |
8 <expand macro="version_command"></expand> | |
9 <command > | |
10 @cat-archiecture@ | |
11 cp $read1_file read1.fastq ; | |
12 cp $read2_file read2.fastq ; | |
13 @tagdust-call-minus-files@ | |
14 read1.fastq read2.fastq ; | |
15 @ls_and_barcode@ | |
16 </command> | |
17 <inputs> | |
18 <param name="read1_file" type="data" format="fastq,fastqsanger" label="Read 1 Fastq file to process" /> | |
19 <param name="read2_file" type="data" format="fastq,fastqsanger" label="Read 2 Fastq file to process" /> | |
20 <expand macro="reference_source"/> | |
21 <expand macro="architecture"/> | |
22 <expand macro="include_barcode_file"/> | |
23 <expand macro="architecture"></expand> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="txt" name="logfile" label="Tagdust log on ${on_string}." from_work_dir="output/data_logfile.txt"/> | |
27 <data format_source="read1_file" name="extracted1" label="Tagdust extracted Read1 from ${on_string}." from_work_dir="output/data_READ1.fq"/> | |
28 <data format_source="read1_file" name="unextracted1" label="Tagdust un-extracted Read1 from ${on_string}." from_work_dir="output/data_un_READ1.fq"/> | |
29 <data format_source="read2_file" name="extracted2" label="Tagdust extracted Read2 from ${on_string}." from_work_dir="output/data_READ2.fq"/> | |
30 <data format_source="read2_file" name="unextracted2" label="Tagdust un-extracted Read2 from ${on_string}." from_work_dir="output/data_un_READ2.fq"/> | |
31 <expand macro="output_barcode"/> | |
32 </outputs> | |
33 <tests> | |
34 <!-- Large dataset in github but not toolshed --> | |
35 <test> | |
36 <param name="read1_file" value="C75_S29_R1_001_extracted.fastq" ftype="fastq" /> | |
37 <param name="read2_file" value="C75_S29_R2_001_extracted.fastq" ftype="fastq" /> | |
38 <param name="architecture" value="R:N" /> | |
39 <param name="reference_source|reference_source_selector" value="history"/> | |
40 <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> | |
41 <output name="logfile" > | |
42 <assert_contents> | |
43 <has_text text="Determining threshold for read0." /> | |
44 </assert_contents> | |
45 </output> | |
46 <output name="extracted1" file="C75_S29__READ1.fq" compare="sim_size" delta="10000"/> | |
47 <output name="unextracted1" file="C75_S29__un_READ1.fq" compare="sim_size" delta="10000"/> | |
48 <output name="extracted2" file="C75_S29__READ2.fq" compare="sim_size" delta="10000"/> | |
49 <output name="unextracted2" file="C75_S29__un_READ2.fq" compare="sim_size" delta="10000"/> | |
50 </test> | |
51 <test> | |
52 <param name="read1_file" value="read1_extracted.fastq" ftype="fastqsanger" /> | |
53 <param name="read2_file" value="read2_extracted.fastq" ftype="fastqsanger" /> | |
54 <param name="architecture" value="test_R:N" /> | |
55 <param name="reference_source|reference_source_selector" value="history"/> | |
56 <param name="reference_source|ref_file" value="ercc_and_TPA_mouse_rRNA.fa" ftype="fasta"/> | |
57 <output name="logfile" > | |
58 <assert_contents> | |
59 <has_text text="Determining threshold for read0." /> | |
60 </assert_contents> | |
61 </output> | |
62 <output name="extracted1" file="paired_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
63 <output name="unextracted1" file="paired_un_READ1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
64 <output name="extracted2" file="paired_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
65 <output name="unextracted2" file="paired_un_READ2.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
66 </test> | |
67 <test> | |
68 <param name="read1_file" value="read1_extracted.fastq" ftype="fastq" /> | |
69 <param name="read2_file" value="read2_extracted.fastq" ftype="fastq" /> | |
70 <param name="architecture" value="test_R:N" /> | |
71 <param name="reference_source|reference_source_selector" value="cached"/> | |
72 <param name="ref_path" value="test_ercc_and_TPA_mouse_RNA"/> | |
73 <output name="logfile" > | |
74 <assert_contents> | |
75 <has_text text="Determining threshold for read0." /> | |
76 </assert_contents> | |
77 </output> | |
78 <output name="extracted1" file="paired_READ1.fq" compare="sim_size" delta="1000"/> | |
79 <output name="unextracted1" file="paired_un_READ1.fq" compare="sim_size" delta="1000"/> | |
80 <output name="extracted2" file="paired_READ2.fq" compare="sim_size" delta="1000"/> | |
81 <output name="unextracted2" file="paired_un_READ2.fq" compare="sim_size" delta="1000"/> | |
82 </test> | |
83 </tests> | |
84 <help> | |
85 <![CDATA[ | |
86 This tool runs Tagdust2 in paired end mode. | |
87 | |
88 ]]> | |
89 @tool-documentation@ | |
90 | |
91 @tagdust-documentation@ | |
92 | |
93 </help> | |
94 <expand macro="citations"></expand> | |
95 </tool> |