Mercurial > repos > brenninc > tagdust_2_31
comparison single.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_single_runner_2_31" name="Tagdust single end runner" version="0.2"> | |
2 <description>Runs tagdust in single end mode</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command > | |
10 @cat-archiecture@ | |
11 cp $fastq_file input.fastq ; | |
12 @tagdust-call-minus-files@ | |
13 input.fastq ; | |
14 @ls_and_barcode@ | |
15 </command> | |
16 <inputs> | |
17 <param name="fastq_file" type="data" format="fastq,fastqsanger" label="Fastq file to process" /> | |
18 <expand macro="reference_source"/> | |
19 <expand macro="architecture"/> | |
20 <expand macro="include_barcode_file"/> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="txt" name="logfile" label="Tagdust log on ${on_string} ." from_work_dir="output/data_logfile.txt"/> | |
24 <data format_source="fastq_file" name="extracted" label="Tagdust extracted reads from ${on_string}." from_work_dir="output/data.fq"/> | |
25 <data format_source="fastq_file" name="unextracted" label="Tagdust un-extracted reads from ${on_string}." from_work_dir="output/data_un.fq"/> | |
26 <expand macro="output_barcode"/> | |
27 </outputs> | |
28 <tests> | |
29 <!-- Large dataset in github but not toolshed --> | |
30 <!--test> | |
31 <param name="fastq_file" value="C75_S29_R1_001.fastq" ftype="fastq" /> | |
32 <param name="architecture" value="F:NNNNNNNN_S:TATAGGG_R:N" /> | |
33 <param name="include|barcode_files" value="no" /> | |
34 <output name="logfile" > | |
35 <assert_contents> | |
36 <has_text text="Determining threshold for read0." /> | |
37 </assert_contents> | |
38 </output> | |
39 <output name="extracted" file="C75_S29_R1_001.fq" compare="sim_size" delta="10000"/> | |
40 <output name="unextracted" file="C75_S29_R1_001_un.fq" compare="sim_size" delta="10000"/> | |
41 </test--> | |
42 <test> | |
43 <param name="fastq_file" value="read1.fastq" ftype="fastqsanger" /> | |
44 <param name="architecture" value="test_F:NNNNNNNN_S:TATAGGG_R:N" /> | |
45 <param name="barcode_files" value="no" /> | |
46 <output name="logfile" > | |
47 <assert_contents> | |
48 <has_text text="Determining threshold for read0." /> | |
49 </assert_contents> | |
50 </output> | |
51 <output name="extracted" file="read1.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
52 <output name="unextracted" file="read1_un.fq" ftype="fastqsanger" compare="sim_size" delta="1000"/> | |
53 </test> | |
54 <test> | |
55 <param name="run_type_selector" value="single"/> | |
56 <param name="fastq_file" value="read1.fastq" ftype="fastq" /> | |
57 <param name="architecture" value="test_B:GTA_AAC_R:N" /> | |
58 <param name="include|barcode_files" value="yes" /> | |
59 <output name="logfile" > | |
60 <assert_contents> | |
61 <has_text text="Determining threshold for read0." /> | |
62 </assert_contents> | |
63 </output> | |
64 <output name="extracted" file="with_b_.fq"/> | |
65 <output name="unextracted" file="with_b_un.fq"/> | |
66 <output name="barcode_files"> | |
67 <assert_contents> | |
68 <has_line line="data_BC_AAC.fq" /> | |
69 <has_line line="data_BC_GTA.fq" /> | |
70 </assert_contents> | |
71 <discovered_dataset designation="AAC" ftype="fastq" file="with_b_BC_AAC.fq"/> | |
72 <discovered_dataset designation="GTA" ftype="fastq" file="with_b_BC_GTA.fq"/> | |
73 </output> | |
74 </test> | |
75 </tests> | |
76 <help> | |
77 <![CDATA[ | |
78 This tool runs Tagdust2 in single mode. | |
79 | |
80 ]]> | |
81 @tool-documentation@ | |
82 | |
83 @tagdust-documentation@ | |
84 | |
85 </help> | |
86 <expand macro="citations"></expand> | |
87 </tool> |