Mercurial > repos > iuc > mageck_count
annotate mageck_count.xml @ 2:9527a3d6ebd2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
| author | iuc |
|---|---|
| date | Wed, 04 Apr 2018 11:03:29 -0400 |
| parents | 4d72d204dcfa |
| children | d8f26ae1e909 |
| 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"?> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
2 <tool id="mageck_count" name="MAGeCK count" version="@VERSION@.2" > |
|
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 = [] |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
16 #for $i, $sample in enumerate($reads.sample): |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
17 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
18 #if $sample.is_of_type('fastq.gz', 'fastqsanger.gz'): |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
19 ln -s '${sample}' input_${i}.gz && |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
20 #set $infile = 'input' + str($i) + '.gz' |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
21 #elif $sample.is_of_type('fastq'): |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
22 ln -s '${sample}' input_${i}.fastq && |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
23 #set $infile = 'input' + str($i) + 'fastq' |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
24 #elif $sample.is_of_type('bam'): |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
25 ln -s '${sample}' input_${i}.bam && |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
26 #set $infile = 'input' + str($i) + 'bam' |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
27 #end if |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
28 #silent $names.append(re.sub('[^\w\-\s]', '_', str($sample.element_identifier))) |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
29 #end for |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
30 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
31 #end if |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
32 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
33 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
34 mageck count |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
35 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
36 #if str($reads.format_select) == "files": |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
37 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
38 -l '$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
|
39 |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
40 --fastq input_* |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
41 |
|
1
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
42 #if $reads.sample_label: |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
43 --sample-label '$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
|
44 #else: |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
45 --sample-label ${ ','.join( $names ) } |
|
1
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
46 #end if |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
47 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
48 #elif str($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
|
49 -k '$reads.counts' |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
50 #if '$sgrna_library_file': |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
51 -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
|
52 #end if |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
53 #end if |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
54 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
55 -n output |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
56 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
57 #if $out.pdfreportOpt: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
58 $out.pdfreportOpt |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
59 --keep-tmp |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
60 #end if |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
61 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
62 $out.unmappedOpt |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
63 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
64 #if $adv.trim5: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
65 --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
|
66 #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
|
67 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
68 #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
|
69 --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
|
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 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
72 #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
|
73 --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
|
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 |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
76 #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
|
77 --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
|
78 #end if |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
79 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
80 $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
|
81 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
82 $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
|
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.test_run |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
85 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
86 #if $adv.gmt_file: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
87 --gmt-file '$adv.gmt_file' |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
88 #end if |
|
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 $out.pdfreportOpt: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
91 && |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
92 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
|
93 #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
|
94 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
95 ]]></command> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
96 <inputs> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
97 <conditional name="reads"> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
98 <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
|
99 <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
|
100 <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
|
101 </param> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
102 <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
|
103 <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
|
104 <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
|
105 <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
|
106 <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
|
107 </param> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
108 </when> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
109 <when value="table"> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
110 <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
|
111 <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
|
112 </when> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
113 </conditional> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
114 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
115 <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
|
116 <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
|
117 <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
|
118 <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
|
119 <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
|
120 <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
|
121 <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
|
122 </section> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
123 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
124 <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
|
125 <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
|
126 <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
|
127 <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
|
128 <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
|
129 <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
|
130 <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
|
131 <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
|
132 </param> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
133 <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
|
134 <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
|
135 <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
|
136 <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
|
137 <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
|
138 </section> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
139 </inputs> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
140 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
141 <outputs> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
142 <data name="counts" format="tabular" from_work_dir="output.count.txt" label="${tool.name} on ${on_string}: sgRNA Counts" /> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
143 <data name="countsummary" format="tabular" from_work_dir="output.countsummary.txt" label="${tool.name} on ${on_string}: sgRNA Count Summary" > |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
144 <filter>out['countsummaryOpt'] is True</filter> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
145 </data> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
146 <data name="normcounts" format="tabular" from_work_dir="output.count_normalized.txt" label="${tool.name} on ${on_string}: Normalized counts" > |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
147 <filter>out['normcountsOpt'] is True or out['rfilesOpt'] is True</filter> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
148 </data> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
149 <data name="unmapped" format="tabular" from_work_dir="output.unmapped.txt" label="${tool.name} on ${on_string}: Unmapped" > |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
150 <filter>out['unmappedOpt'] is True</filter> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
151 </data> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
152 <data name="pdfreport" format="pdf" from_work_dir="merged.pdf" label="${tool.name} on ${on_string}: PDF Report" > |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
153 <filter>out['pdfreportOpt'] is True</filter> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
154 </data> |
|
1
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
155 <data name="log" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log" > |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
156 <filter>out['logOpt'] is True</filter> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
157 </data> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
158 <data name="rscript" format="txt" from_work_dir="output_countsummary.R" label="${tool.name} on ${on_string}: R file" > |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
159 <filter>out['rfilesOpt'] is True</filter> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
160 </data> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
161 <data name="rnwfile" format="txt" from_work_dir="output_countsummary.Rnw" label="${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
|
162 <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
|
163 </data> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
164 </outputs> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
165 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
166 <tests> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
167 <!-- 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
|
168 <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
|
169 <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
|
170 <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
|
171 <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
|
172 <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
|
173 </test> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
174 <!-- 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
|
175 <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
|
176 <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
|
177 <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
|
178 <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
|
179 <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
|
180 <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
|
181 <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
|
182 </test> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
183 <!-- Ensure fastq input works --> |
|
1
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
184 <test expect_num_outputs="1"> |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
185 <param name="sgrna_library_file" value="demo/demo2/library.txt" ftype="tabular" /> |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
186 <param name="format_select" value="files" /> |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
187 <param name="sample" value="demo/demo2/test1.fastq" ftype="fastq"/> |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
188 <param name="sample_label" value="test1_fastq_gz" /> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
189 <output name="counts" file="out.count.txt"/> |
|
1
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
190 </test> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
191 <!-- 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
|
192 <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
|
193 <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
|
194 <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
|
195 <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
|
196 <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
|
197 </test> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
198 <!-- 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
|
199 <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
|
200 <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
|
201 <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
|
202 <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
|
203 <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
|
204 <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
|
205 <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
|
206 <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
|
207 <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
|
208 <output name="counts" file="out.count.fastq.txt"/> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
209 <output name="countsummary" file="out.countsummary.txt" 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
|
210 <output name="normcounts" file="output.count_normalized.txt"/> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
211 <output name="log" file="out.count.log.txt" compare="sim_size"/> |
|
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" /> |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
215 <output name="rnwfile" file="output_countsummary.Rnw" /> |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
216 </test> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
217 </tests> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
218 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
219 <help><![CDATA[ |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
220 .. class:: infomark |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
221 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
222 **What it does** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
223 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
224 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
|
225 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
226 ----- |
|
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 **Inputs** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
229 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
230 **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
|
231 |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
232 **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
|
233 |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
234 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
|
235 |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
236 * 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
|
237 * 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
|
238 * 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
|
239 |
|
4d72d204dcfa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7
iuc
parents:
0
diff
changeset
|
240 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
|
241 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
242 **sgRNA library file** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
243 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
244 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
|
245 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
246 Example: |
|
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 ============ ==================== ======== |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
249 **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
|
250 ------------ -------------------- -------- |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
251 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
|
252 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
|
253 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
|
254 ============ ==================== ======== |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
255 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
256 **Control sgRNA file** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
257 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
258 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
|
259 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
260 ----- |
|
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 **Outputs** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
263 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
264 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
|
265 |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
266 * 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
|
267 |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
268 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
|
269 |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
270 * 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
|
271 * 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
|
272 * 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
|
273 * 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
|
274 * 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
|
275 * 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
|
276 |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
277 **sgRNA Count file** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
278 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
279 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
|
280 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
281 Example: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
282 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
283 ============== ======== =========== =========== |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
284 **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
|
285 -------------- -------- ----------- ----------- |
|
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
286 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
|
287 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
|
288 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
|
289 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
|
290 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
|
291 ============== ======== =========== =========== |
|
0
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
292 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
293 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
294 **Count Summary** |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
295 |
|
2
9527a3d6ebd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 49e456dda49db1f52fc876f406a10273a408b1a2
iuc
parents:
1
diff
changeset
|
296 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
|
297 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
298 Example: |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
299 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
300 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============ |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
301 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
|
302 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============ |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
303 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
|
304 ========== ===== ===== ====== ========== =========== ========== ========= ======== ============ ======================= ========================== ============ |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
305 |
|
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 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
308 **More Information** |
|
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 **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
|
311 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
312 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
|
313 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
314 **MAGeCK FAQs** |
|
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 **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
|
317 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
|
318 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
|
319 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
320 **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
|
321 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
|
322 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
323 **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
|
324 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
|
325 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
326 #. 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
|
327 #. 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
|
328 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
329 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
|
330 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
331 .. _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
|
332 .. _`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
|
333 .. _`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
|
334 .. _`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
|
335 |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
336 ]]></help> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
337 <expand macro="citations" /> |
|
b80c0e046539
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 71cef018eec5ee7ff7f3853599c027e80e2637fe
iuc
parents:
diff
changeset
|
338 </tool> |