Mercurial > repos > iuc > pretext_map

annotate pretext_map.xml @ 4:bbe19ef04a74 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
author iuc
date Thu, 11 Nov 2021 15:05:34 +0000
parents d256a51a656b
children 2b16ba799da9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
2 <description>converts SAM or BAM files into genome contact maps</description>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
3 <macros>
3
d256a51a656b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 66f812cf66b8e2f26ca4c4a607c621576ce4ed42"
iuc
parents: 2
diff changeset
4 <token name="@TOOL_VERSION@">0.1.8</token>
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
6 </macros>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
7 <requirements>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
2
8fef980d48b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 474777450e3f847cb9badb020b56469f226546da"
iuc
parents: 1
diff changeset
9 <requirement type="package" version="1.13">samtools</requirement>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
10 </requirements>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
11 <version_command>PretextMap --version</version_command>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
13 #if $input.is_of_type("bam"):
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
14 samtools view -h '${input}' |
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
15 #else
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
16 cat '${input}' |
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
17 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
18 PretextMap
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
19 #if $sorting.sortby == "length":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
20 --sortby length
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
21 --sortorder $sorting.sortorder
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
22 #elif $sorting.sortby == "name":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
23 --sortby name
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
24 --sortorder $sorting.sortorder
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
25 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
26 #if $map_qual:
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
27 --mapq $map_qual
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
28 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
29 #if $filter.filter_type == "in":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
30 --filterInclude '$filter.filter_list'
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
31 #elif $filter.filter_type == "out":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
32 --filterExclude '$filter.filter_list'
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
33 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
34 -o output.pretext
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
35 ]]></command>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
36 <inputs>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
37 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
38 <conditional name="sorting">
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
39 <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds">
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
40 <option value="nosort">Don't sort</option>
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
41 <option value="length" selected="true">Length</option>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
42 <option value="name">Name</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
43 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
44 <when value="nosort"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
45 <when value="length">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
46 <param argument="--sortorder" type="select" label="Sort order: ">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
47 <option value="ascend">Ascending</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
48 <option value="decend">Decending</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
49 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
50 </when>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
51 <when value="name">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
52 <param argument="--sortorder" type="select" label="Sort order: ">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
53 <option value="ascend">Ascending</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
54 <option value="descend">Decending</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
55 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
56 </when>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
57 </conditional>
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
58 <param name="map_qual" argument="--mapq" type="integer" label="Minimum mapping quality:" min="0" value="10" optional="true" help=" Filter mapped read by minimum MAPQ. Useful to remove spurious contacts from multimapping reads"/>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
59 <conditional name="filter">
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
60 <param name="filter_type" type="select" label="How to filter: " help="Subset the output excluding a list of scaffolds">
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
61 <option value="" selected="true">No filter</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
62 <option value="in">Filter to include only specified sequence names</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
63 <option value="out">Filter to exclude specified sequence names</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
64 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
65 <when value=""/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
66 <when value="in">
1
02831bf9e95f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
iuc
parents: 0
diff changeset
67 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
68 <sanitizer>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
69 <valid initial="string.ascii_letters,string.digits">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
70 <add value="_"/>
1
02831bf9e95f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
iuc
parents: 0
diff changeset
71 <add value=","/>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
72 </valid>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
73 </sanitizer>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
74 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
75 </when>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
76 <when value="out">
1
02831bf9e95f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
iuc
parents: 0
diff changeset
77 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
78 <sanitizer>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
79 <valid initial="string.ascii_letters,string.digits">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
80 <add value="_"/>
1
02831bf9e95f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
iuc
parents: 0
diff changeset
81 <add value=","/>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
82 </valid>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
83 </sanitizer>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
84 </param>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
85 </when>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
86 </conditional>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
87 </inputs>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
88 <outputs>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
89 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
90 </outputs>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
91 <tests>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
92 <test>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
93 <param name="input" ftype="bam" value="test.bam"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
94 <conditional name="sorting">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
95 <param name="sortby" value="length"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
96 <param name="sortorder" value="ascend"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
97 </conditional>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
98 <conditional name="filter">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
99 <param name="filter_type" value="in"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
100 <param name="filter_list" value="ref"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
101 </conditional>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
102 <param name="map_qual" value="10"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
103 <output name="pretext_map_out" file="output_1.pretext"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
104 </test>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
105 <test>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
106 <param name="input" ftype="sam" value="test.sam"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
107 <conditional name="sorting">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
108 <param name="sortby" value="name"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
109 <param name="sortorder" value="descend"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
110 </conditional>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
111 <conditional name="filter">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
112 <param name="filter_type" value="out"/>
1
02831bf9e95f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
iuc
parents: 0
diff changeset
113 <param name="filter_list" value="chrM,chr8,chr9"/>
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
114 </conditional>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
115 <output name="pretext_map_out" file="output_2.pretext"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
116 </test>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
117 </tests>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
118 <help><![CDATA[
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
119
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
120 **What is does**
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
121
4
bbe19ef04a74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 21b72bf355117b1b6cf0fb13fa34139395409011"
iuc
parents: 3
diff changeset
122 PretextMap (Paired REad TEXTure Mapper) converts SAM/BAM/CRAM or `pairs files <https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md>`_ into `genome contact maps <https://genome.ucsc.edu/goldenPath/help/hic.html>`_.
0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
123
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
124 ]]></help>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
125 <citations>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
126 <citation type="bibtex">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
127 @misc{Harry_et_al,
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
128 Author={Harry, E},
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
129 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
130 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
131 </citation>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
132 </citations>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
parents:
diff changeset
133 </tool>