annotate mageck_count.xml @ 6:3edbd1ff5602 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 0c76d2d8677e66d4f76ac748614c7911f298758c
author iuc
date Sat, 05 Jan 2019 05:48:56 -0500
parents 3bcf77e9c7e3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
5
3bcf77e9c7e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
iuc
parents: 4
diff changeset
2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.4" >
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
3 <description>- collect sgRNA read counts from read mapping files</description>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
4 <macros>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
5 <import>mageck_macros.xml</import>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
6 </macros>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
7 <expand macro="requirements">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
8 <requirement type="package" version="9.22">ghostscript</requirement>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
9 </expand>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
10 <expand macro="version" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
12
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
13 #if str($reads.format_select) == "files":
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
14 #import re
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
15 #set $names = []
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
16 #set $files = []
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
17
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
18 #for $sample in $reads.sample:
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
19
5
3bcf77e9c7e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
iuc
parents: 4
diff changeset
20 #set name = re.sub('[^\w\-\.]', '_', str($sample.element_identifier))
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
21
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
22 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'):
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
23 #set infile = $name + ".fq.gz"
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
24 #elif $sample.is_of_type('fastq'):
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
25 #set infile = $name + ".fq"
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
26 #elif $sample.is_of_type('bam'):
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
27 #set infile = $name + ".bam"
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
28 #end if
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
29
4
bb6b6af01920 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 1ec61a5000b70303a3655de0a74bcd52cd4b9d02
iuc
parents: 3
diff changeset
30 ln -s '${sample}' '$infile' &&
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
31
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
32 #silent $files.append($infile)
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
33 #silent $names.append($name)
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
34
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
35 #end for
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
36 #end if
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
37
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
38 mageck count
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
39
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
40 #if str($reads.format_select) == "files":
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
41
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
42 -l '$reads.sgrna_library_file'
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
43
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
44 --fastq ${ ' '.join( ["'%s'" % $x for $x in $files] ) }
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
45
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
46 #if $reads.sample_label:
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
47 --sample-label '$reads.sample_label'
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
48 #else:
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
49 --sample-label ${ ','.join( ["'%s'" % $x for $x in $names] ) }
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
50 #end if
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
51
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
52 #elif str($reads.format_select) == "table":
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
53 -k '$reads.counts'
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
54 #if '$sgrna_library_file':
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
55 -l '$sgrna_library_file'
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
56 #end if
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
57 #end if
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
58
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
59 -n output
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
60
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
61 #if $out.pdfreportOpt:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
62 $out.pdfreportOpt
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
63 --keep-tmp
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
64 #end if
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
65
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
66 $out.unmappedOpt
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
67
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
68 #if $adv.trim5:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
69 --trim-5 $adv.trim5
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
70 #end if
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
71
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
72 #if $adv.norm_method:
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
73 --norm-method $adv.norm_method
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
74 #end if
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
75
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
76 #if $adv.control_sgrna:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
77 --control-sgrna $adv.control_sgrna
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
78 #end if
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
79
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
80 #if $adv.sgrna_len:
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
81 --sgrna-len $adv.sgrna_len
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
82 #end if
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
83
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
84 $adv.count_n
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
85
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
86 $adv.reverse_complement
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
87
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
88 $adv.test_run
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
89
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
90 #if $adv.gmt_file:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
91 --gmt-file '$adv.gmt_file'
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
92 #end if
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
93
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
94 #if $out.pdfreportOpt:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
95 &&
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
96 gs -dBATCH -dNOPAUSE -q -dPDFSETTINGS=/prepress -sDEVICE=pdfwrite -sOutputFile=merged.pdf *.pdf
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
97 #end if
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
98
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
99 ]]></command>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
100 <inputs>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
101 <conditional name="reads">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
102 <param name="format_select" type="select" label="Reads Files or Count Table?" help="You can choose to input either separate files of reads (one per sample) or a single count table">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
103 <option value="files">Separate Reads files</option>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
104 <option value="table">Single Count table</option>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
105 </param>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
106 <when value="files">
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
107 <param name="sample" argument="--fastq" type="data" format="fastq,fastq.gz,bam" multiple="true" label="Sample reads" help="The input reads must be in FASTQ, FASTQ.GZ or BAM format and all files must be in the same format." />
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
108 <param name="sgrna_library_file" type="data" argument="--list-seq" format="txt,tabular,tsv,csv" label="sgRNA library file" help="A library file must be provided with three columns containing the sgRNA ID, sequence, and gene it is targeting, see Help below for more information." />
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
109 <param name="sample_label" argument="--sample-label" type="text" optional="true" value="" label="Specify sample labels" help="By default, the input filenames will be used as the sample labels. Optionally you can specify different sample labels to use which must be separated by comma (,). Must be equal to the number of samples provided in --fastq option.">
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
110 <validator type="regex" message="Please only use letters, numbers or underscores in sample labels, and separate labels by commas">^[\w,]+$</validator>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
111 </param>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
112 </when>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
113 <when value="table">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
114 <param name="counts" argument="-k" type="data" format="tabular" optional="true" label="Counts Table" help="Alternatively, a tab-separated file of read counts can be used as input. See Help below for format" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
115 <param name="sgrna_library_file" type="data" argument="--list-seq" format="txt,tabular,tsv,csv" optional="True" label="sgRNA library file" help="Optionally, a library file can be provided with three columns containing the sgRNA ID, sequence, and gene it is targeting, see Help below for more information." />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
116 </when>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
117 </conditional>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
118
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
119 <section name="out" title="Output Options">
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
120 <param name="countsummaryOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output Count Summary file" help="Output summary statistics of the fastq files. Default: No" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
121 <param name="normcountsOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output Normalized Counts file" help="Default: No" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
122 <param name="pdfreportOpt" argument="--pdf-report" type="boolean" truevalue="--pdf-report" falsevalue="" checked="false" optional="true" label="Output plots" help="Generate PDF of the plots. Default: No" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
123 <param name="unmappedOpt" argument="--unmapped-to-file" type="boolean" truevalue="--unmapped-to-file" falsevalue="" checked="false" optional="true" label="Output Unmapped reads" help="Save nmapped reads to file. Default: No" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
124 <param name="rfilesOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output R files" help="Output the .R and .Rnw files used to generate the plots in the PDF report. The median-normalized read counts file will also be output as it is required to regenerate the plots. Default: No" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
125 <param name="logOpt" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output Log file" help="This file includes the logging information, it will list some basic statistics of the dataset at the end. Default: No" />
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
126 </section>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
127
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
128 <section name="adv" title="Advanced Options">
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
129 <param name="gmt_file" argument="--gmt-file" type="data" format="tabular" optional="true" value="" label="Pathway file for QC" help="The pathway file used for QC, in GMT format. By default it will use the GMT file provided by MAGeCK" />
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
130 <param name="trim5" argument="--trim-5" type="integer" min="0" optional="true" label="5' Trim length" help="Length of trimming the 5' of the reads. Default: 0" />
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
131 <param name="norm_method" argument="--norm-method" type="select" optional="true" label="Method for normalization" help="Methods include: None (no normalization), Median (median normalization), Total (normalization by total read counts), Control (normalization by control sgRNAs specified by the --control-sgrna option). Default: Median" >
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
132 <option value="median" selected="True">Median</option>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
133 <option value="none">None</option>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
134 <option value="total">Total</option>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
135 <option value="control">Control</option>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
136 </param>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
137 <param name="control_sgrna" argument="--control-sgrna" type="data" format="tabular" optional="true" label="Control sgRNAs file" help="A file of control sgRNA IDs for normalization and for generating the null distribution of RRA" />
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
138 <param name="sgrna_len" argument="--sgrna-len" type="integer" min="0" optional="true" label="Length of the sgRNA" help="The program will automatically determine the sgRNA length from the library file, so only use this if you turn on the --unmapped-to-file option. Default: autodetected" />
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
139 <param name="count_n" argument="--count-n" type="boolean" truevalue="--count-n" falsevalue="" checked="false" optional="true" label="Count sgRNAs with Ns" help="By default, sgRNAs containing Ns will be discarded" />
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
140 <param name="reverse_complement" argument="--reverse-complement" type="boolean" truevalue="--reverse-complement" falsevalue="" checked="false" optional="true" label="Reverse complement" help="Reverse complement the sequences in library for read mapping" />
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
141 <param name="test_run" argument="--test-run" type="boolean" truevalue="--test-run" falsevalue="" checked="false" optional="true" label="Test running" help="If this option is on, MAGeCK will only process the first 1M records for each file" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
142 </section>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
143 </inputs>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
144
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
145 <outputs>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
146 <data name="counts" format="tabular" from_work_dir="output.count.txt" label="${tool.name} on ${on_string}: sgRNA Counts" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
147 <data name="countsummary" format="tabular" from_work_dir="output.countsummary.txt" label="${tool.name} on ${on_string}: sgRNA Count Summary" >
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
148 <filter>out['countsummaryOpt'] is True</filter>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
149 </data>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
150 <data name="normcounts" format="tabular" from_work_dir="output.count_normalized.txt" label="${tool.name} on ${on_string}: Normalized counts" >
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
151 <filter>out['normcountsOpt'] is True or out['rfilesOpt'] is True</filter>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
152 </data>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
153 <data name="unmapped" format="tabular" from_work_dir="output.unmapped.txt" label="${tool.name} on ${on_string}: Unmapped" >
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
154 <filter>out['unmappedOpt'] is True</filter>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
155 </data>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
156 <data name="pdfreport" format="pdf" from_work_dir="merged.pdf" label="${tool.name} on ${on_string}: PDF Report" >
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
157 <filter>out['pdfreportOpt'] is True</filter>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
158 </data>
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
159 <data name="log" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log" >
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
160 <filter>out['logOpt'] is True</filter>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
161 </data>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
162 <data name="rscript" format="txt" from_work_dir="output_countsummary.R" label="${tool.name} on ${on_string}: R file" >
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
163 <filter>out['rfilesOpt'] is True</filter>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
164 </data>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
165 <data name="rnwfile" format="txt" from_work_dir="output_countsummary.Rnw" label="${tool.name} on ${on_string}: Rnw file" >
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
166 <filter>out['rfilesOpt'] is True</filter>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
167 </data>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
168 </outputs>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
169
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
170 <tests>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
171 <!-- Ensure fastq.gz input works -->
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
172 <test expect_num_outputs="1">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
173 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
174 <param name="format_select" value="files" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
175 <param name="sample" value="test1.fastq.gz" ftype="fastq.gz"/>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
176 <output name="counts" file="out.count.txt"/>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
177 </test>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
178 <!-- Ensure multiple fastq.gz input works with report -->
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
179 <test expect_num_outputs="2">
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
180 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
181 <param name="format_select" value="files" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
182 <param name="sample" value="test1.fastq.gz,test2.fastq.gz" ftype="fastq.gz"/>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
183 <param name="pdfreportOpt" value="True" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
184 <output name="counts" file="out.count_multi.txt"/>
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
185 <output name="pdfreport" file="out.countsummary_multi.pdf" compare="sim_size" />
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
186 </test>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
187 <!-- Ensure BAM input works -->
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
188 <test expect_num_outputs="1">
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
189 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
190 <param name="format_select" value="files" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
191 <param name="sample" value="test1.bam" ftype="bam"/>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
192 <output name="counts" file="out.count.bam.txt"/>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
193 </test>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
194 <!-- Ensure optional outputs work -->
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
195 <test expect_num_outputs="8">
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
196 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
197 <param name="format_select" value="files" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
198 <param name="sample" value="test1.fastq.gz" ftype="fastq.gz"/>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
199 <param name="countsummaryOpt" value="True" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
200 <param name="unmappedOpt" value="True" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
201 <param name="pdfreportOpt" value="True" />
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
202 <param name="rfilesOpt" value="True" />
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
203 <param name="logOpt" value="True" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
204 <output name="counts" file="out.count.fastq.txt"/>
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
205 <output name="countsummary" file="out.countsummary.txt" compare="contains"/>
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
206 <output name="normcounts" file="output.count_normalized.txt"/>
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
207 <output name="log">
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
208 <assert_contents>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
209 <has_text_matching expression="Welcome to MAGeCK"/>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
210 </assert_contents>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
211 </output>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
212 <output name="unmapped" file="out.count.unmapped.txt" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
213 <output name="pdfreport" file="out.countsummary.pdf" compare="sim_size" />
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
214 <output name="rscript" file="out.count.R" />
3
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
215 <output name="rnwfile">
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
216 <assert_contents>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
217 <has_text_matching expression="This is a template file for Sweave"/>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
218 </assert_contents>
d8f26ae1e909 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 95daf3f97e89989bae687e64cae8b129b3e2b7af
iuc
parents: 2
diff changeset
219 </output>
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
220 </test>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
221 </tests>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
222
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
223 <help><![CDATA[
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
224 .. class:: infomark
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
225
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
226 **What it does**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
227
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
228 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK_) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK can be used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK identifies both positively and negatively selected genes simultaneously and reports robust results across different experimental conditions. MAGeCK is developed and maintained by Wei Li and Han Xu from `Prof. Xiaole Shirley Liu's lab`_ at the Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health. MAGeCK has been used to identify functional lncRNAs from screens with close to `100% validation rate`_.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
229
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
230 -----
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
231
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
232 **Inputs**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
233
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
234 **Read files**
1
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
235
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
236 **MAGeCK count** accepts one or more FASTQ.GZ, FASTQ or BAM files as input.
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
237
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
238 Since version 0.5.5, MAGeCK count module supports collecting read counts from BAM files. This will allow you to use a third-party aligner to map reads to the library with mismatches, providing more usable reads for the analysis. However, it is still recommended to directly use the fastq file in the count module (which does not allow any mismatches), because:
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
239
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
240 * Some mismatches in the sgRNAs may have unwanted behaviors (have no on-target cleavages or have other off-target cleavages);
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
241 * In most cases the read counts are enough if we allow no mismatches;
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
242 * The mapping procedure is more complicated; for example, you need to know the exact length of 3' adapter sequence.
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
243
4d72d204dcfa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents: 0
diff changeset
244 It is also possible to input a Count Table to normalize counts and get statistics.
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
245
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
246 **sgRNA library file**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
247
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
248 When starting from FASTQ, FASTQ.GZ or BAM files, MAGeCK needs to know the sgRNA sequences and targeting genes. Such information is provided in the sgRNA library file and can be specified in the tool form above. The sgRNA library file can be provided in .tsv or .csv format. There are three columns in the library file: the sgRNA ID, the sequence, and the gene it is targeting.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
249
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
250 Example:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
251
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
252 ============ ==================== ========
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
253 **sgRNA ID** **Sequence** **Gene**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
254 ------------ -------------------- --------
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
255 s_10007 TGTTCACAGTATAGTTTGCC CCNA1
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
256 s_10008 TTCTCCCTAATTGCTTGCTG CCNA1
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
257 s_10027 ACATGTTGCTTCCCCTTGCA CCNC
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
258 ============ ==================== ========
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
259
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
260 **Control sgRNA file**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
261
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
262 The optional Control sgRNAs file is used to generate null distribution when calculating the p values. If this option is not specified, MAGeCK generates the null distribution of RRA scores by assuming all of the genes in the library are non-essential, see **More Information** below. This approach is sometimes over-conservative, and you can improve this if you know some genes are not essential. By providing the corresponding sgRNA IDs in this option, MAGeCK will have a better estimation of p values. To use this option, you need to prepare a text file specifying the IDs of control sgRNAs, one line for one sgRNA ID.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
263
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
264 -----
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
265
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
266 **Outputs**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
267
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
268 This tool outputs
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
269
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
270 * an sgRNA Counts table
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
271
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
272 Optionally, under **Output Options** you can choose to output
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
273
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
274 * a Count Summary file
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
275 * a PDF report
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
276 * a Normalized Counts table
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
277 * an Unmapped reads file
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
278 * the .R and .Rnw files used to generate the plots and PDF
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
279 * a Log file of the analysis
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
280
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
281 **sgRNA Count file**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
282
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
283 An example of the sgRNA count output file is shown below. This file can be used with **MAGeCK test**.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
284
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
285 Example:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
286
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
287 ============== ======== =========== ===========
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
288 **sgRNA** **Gene** **Sample1** **Sample2**
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
289 -------------- -------- ----------- -----------
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
290 A1CF_m52595977 A1CF 213 199
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
291 A1CF_m52596017 A1CF 294 164
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
292 A1CF_m52596056 A1CF 421 378
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
293 A1CF_m52603842 A1CF 274 281
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
294 A1CF_m52603847 A1CF 0 0
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
295 ============== ======== =========== ===========
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
296
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
297
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
298 **Count Summary**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
299
2
9527a3d6ebd2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents: 1
diff changeset
300 MAGeCK can produce a **Count Summary** file containing statistics of the input files (the statistics of fastq files are also in the PDF report). An example count summary file is shown below.
0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
301
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
302 Example:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
303
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
304 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
305 File Label Reads Mapped Percentage TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation NegSelQCPvalPermutationFDR NegSelQCGene
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
306 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
307 InputFile1 L1 2500 1453 0.5812 2550 1276 0.5267 0 1 1 1 0.0
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
308 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
309
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
310 -----
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
311
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
312 **More Information**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
313
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
314 **Overview of the MAGeCK algorithm**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
315
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
316 Briefly, read counts from different samples are first median-normalized to adjust for the effect of library sizes and read count distributions. Then the variance of read counts is estimated by sharing information across features, and a negative binomial (NB) model is used to test whether sgRNA abundance differs significantly between treatments and controls. This approach is similar to those used for differential RNA-Seq analysis. We rank sgRNAs based on P-values calculated from the NB model, and use a modified robust ranking aggregation (RRA) algorithm named α-RRA to identify positively or negatively selected genes. More specifically, α-RRA assumes that if a gene has no effect on selection, then sgRNAs targeting this gene should be uniformly distributed across the ranked list of all the sgRNAs. α-RRA ranks genes by comparing the skew in rankings to the uniform null model, and prioritizes genes whose sgRNA rankings are consistently higher than expected. α-RRA calculates the statistical significance of the skew by permutation, and a detailed description of the algorithm is presented in the Materials and methods section of the MAGeCK paper. Finally, MAGeCK reports positively and negatively selected pathways by applying α-RRA to the rankings of genes in a pathway.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
317
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
318 **MAGeCK FAQs**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
319
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
320 **The 5' trim length option can only trim a fixed length of nucleotides before sgRNA, but what if the trimming length is different in different reads?**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
321 MAGeCK enables automatically determining trimming length, even the length may be different within the same fastq files.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
322 Alternatively, you can use **cutadapt** to trim the adaptor sequences of variable length before running MAGeCK.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
323
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
324 **How do I get the simple statistics of my input files?**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
325 MAGeCK produces a **Count Summary** file containing the statistics of the input files, the statistics are also in the PDF report. The statistics can also be found in the log file for **MAGeCK** count.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
326
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
327 **How do I know the quality of my samples?**
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
328 For simple QC terms, you can just take a look at the sample statistics. Generally in a good negative selection sample:
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
329
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
330 #. the mapped reads should be over 60 percent of the total number reads
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
331 #. the number of zero-count sgRNAs should be few (<5%, and prefered <1%). One exception is in positive selection experiments, where the number of zero-count sgRNAs may be much higher, but the percentage of mapped reads should be reasonably high.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
332
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
333 For more information on using MAGeCK, see the `MAGeCK website here`_.
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
334
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
335 .. _MAGeCK: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0554-4
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
336 .. _`100% validation rate`: https://sourceforge.net/p/mageck/wiki/Home/
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
337 .. _`Prof. Xiaole Shirley Liu's lab`: http://liulab.dfci.harvard.edu/
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
338 .. _`MAGeCK website here`: https://sourceforge.net/p/mageck/wiki/QA/#using-mageck
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
339
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
340 ]]></help>
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
341 <expand macro="citations" />
b80c0e046539 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff changeset
342 </tool>