Mercurial > repos > iuc > crossmap_bam

annotate crossmap_bam.xml @ 11:8f5580caf79b draft default tip

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/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 11:59:42 +0000
parents c413cbb69f3c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
acd53aae2d46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
iuc
parents: 5
diff changeset
1 <tool id="crossmap_bam" name="CrossMap BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
3 <macros>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
4 <import>macros.xml</import>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
5 </macros>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
9 <command><![CDATA[
5
c76b5389bb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
parents: 4
diff changeset
10
c76b5389bb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
parents: 4
diff changeset
11 ln -s '${input}' ./input.bam &&
c76b5389bb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
parents: 4
diff changeset
12
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
13 CrossMap bam
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
14 '${chain_source.input_chain}'
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
15 $optional_tags
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
16
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
17 -m $insert_size
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
18 -s $insert_size_stdev
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
19 -t $insert_size_fold
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
20
5
c76b5389bb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 2dbcf8154aff86b27a1dd535407d20168c4ef697"
iuc
parents: 4
diff changeset
21 ./input.bam
4
dde84a63f767 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
iuc
parents: 3
diff changeset
22 output
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
23 ]]></command>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
24 <inputs>
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
25 <param name="input" type="data" format="bam" label="BAM file"/>
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
26 <expand macro="chain"/>
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
27 <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/>
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
28 <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/>
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
29 <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/>
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
30 <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/>
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
31 </inputs>
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
32 <outputs>
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
33 <data name="output" format="bam" label="${tool.name} on ${on_string}" from_work_dir="output.sorted.bam"/>
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
34 <!-- CrossMap 0.2.5 does not produce output_unmapped -->
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
35 </outputs>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
36 <tests>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
37 <test>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
38 <param name="index_source" value="history"/>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
39 <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
40 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
41 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
42 </test>
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
43 <test>
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
44 <param name="index_source" value="cached"/>
3
d2c1f9f2cd0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
iuc
parents: 2
diff changeset
45 <param name="input" value="test_bam_01_input_a.bam" ftype="bam" dbkey="hg18"/>
11
8f5580caf79b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
iuc
parents: 9
diff changeset
46 <output name="output" file="test_bam_01_output_a.bam" ftype="bam" lines_diff="6"/>
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
47 </test>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
48 </tests>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
49 <help><![CDATA[
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
50 @HELP_GENERAL@
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
51
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
52 BAM
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
53 ---------
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
54
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
55 CrossMap updates chromosomes, genome coordinates, header sections, and all
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
56 BAM flags accordingly. The program version (of CrossMap) is inserted into the
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
57 header section, along with the names of the original BAM file and the chain
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
58 file. For pair-end sequencing, insert size is also recalculated.
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
59
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
60
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
61 **Optional tags**
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
62
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
63 Q
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
64 QC. QC failed.
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
65
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
66 N
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
67 Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
68
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
69 M
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
70 Multiple mapped. Alignment can be liftover to multiple places.
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
71
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
72 U
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
73 Unique mapped. Alignment can be liftover to only 1 place.
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
74
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
75 **Tags for pair-end sequencing include:**
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
76
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
77 QF
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
78 QC failed
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
79 NN
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
80 both read1 and read2 unmapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
81 NU
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
82 read1 unmapped, read2 unique mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
83 NM
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
84 read1 unmapped, multiple mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
85 UN
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
86 read1 uniquely mapped, read2 unmap
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
87 UU
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
88 both read1 and read2 uniquely mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
89 UM
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
90 read1 uniquely mapped, read2 multiple mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
91 MN
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
92 read1 multiple mapped, read2 unmapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
93 MU
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
94 read1 multiple mapped, read2 unique mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
95 MM
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
96 both read1 and read2 multiple mapped
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
97
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
98 **Tags for single-end sequencing include**
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
99
2
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
100 QF
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
101 QC failed
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
102 SN
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
103 unmaped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
104 SM
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
105 multiple mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
106 SU
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
107 uniquely mapped
6463cf32d733 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
108 ]]></help>
0
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
109 <citations>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
110 <citation type="doi">10.1093/bioinformatics/btt730</citation>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
111 </citations>
9bcfe0aabf5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
112 </tool>