Mercurial > repos > drosofff > msp_sr_bowtie_cascade
annotate sRbowtieCascade.xml @ 0:0528fced93a9 draft default tip
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author | drosofff |
---|---|
date | Wed, 27 May 2015 17:31:35 -0400 |
parents | |
children |
rev | line source |
---|---|
0
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
2 <description>Using iterative sRbowtie Alignments</description> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
3 <requirements> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
4 <requirement type="package" version="0.12.7">bowtie</requirement> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
5 </requirements> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
6 <command interpreter="python"> sRbowtieCascade.py --output $output |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
7 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
8 --mismatch $mismatches |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
9 --input |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
10 #for $i in $input: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
11 $i |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
12 #end for |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
13 --label |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
14 #for $i in $input: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
15 "$i.name" |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
16 #end for |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
17 --index |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
18 #if $refGenomeSource1.genomeSource == "history": |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
19 $refGenomeSource1.ownFile |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
20 #else: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
21 $refGenomeSource1.index.fields.path |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
22 #end if |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
23 #for $i in $AdditionalQueries: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
24 #if $i.refGenomeSource.genomeSource == "history": |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
25 $i.refGenomeSource.ownFile |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
26 #else: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
27 $i.refGenomeSource.index.fields.path |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
28 #end if |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
29 #end for |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
30 --indexing-flags |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
31 $refGenomeSource1.genomeSource |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
32 #for $i in $AdditionalQueries: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
33 $i.refGenomeSource.genomeSource |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
34 #end for |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
35 --indexName |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
36 #if $refGenomeSource1.genomeSource == "history": |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
37 "$refGenomeSource1.ownFile.name" |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
38 #else: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
39 "$refGenomeSource1.index.fields.name" |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
40 #end if |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
41 #for $i in $AdditionalQueries: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
42 #if $i.refGenomeSource.genomeSource == "history": |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
43 "$i.refGenomeSource.ownFile.name" |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
44 #else: |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
45 "$i.refGenomeSource.index.fields.name" |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
46 #end if |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
47 #end for |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
48 </command> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
49 <inputs> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
50 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files" multiple="true"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
51 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
52 <option value="0">0</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
53 <option value="1" selected="true">1</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
54 <option value="2">2</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
55 <option value="3">3</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
56 </param> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
57 <!-- First bowtie index selection --> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
58 <conditional name="refGenomeSource1"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
59 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
60 <option value="indexed">Use a built-in index</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
61 <option value="history">Use one from the history</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
62 </param> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
63 <when value="indexed"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
64 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
65 <options from_data_table="bowtie_indexes"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
66 </param> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
67 </when> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
68 <when value="history"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
69 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
70 </when> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
71 </conditional> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
72 <!-- End of first bowtie index selection --> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
73 <!-- other bowtie index selections --> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
74 <repeat name="AdditionalQueries" title="Additional Alignment Step"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
75 <conditional name="refGenomeSource"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
76 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
77 <option value="indexed">Use a built-in index</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
78 <option value="history">Use one from the history</option> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
79 </param> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
80 <when value="indexed"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
81 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
82 <options from_data_table="bowtie_indexes"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
83 </param> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
84 </when> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
85 <when value="history"> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
86 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
87 </when> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
88 </conditional> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
89 </repeat> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
90 <!-- End of other bowtie index selections --> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
91 </inputs> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
92 <outputs> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
93 <data format="tabular" name="output" label="Cascade Annotation Analysis"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
94 </outputs> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
95 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
96 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
97 <tests> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
98 <test> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
99 <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
100 <param name="genomeSource" value="history" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
101 <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
102 <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
103 <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
104 <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
105 <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
106 <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" /> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
107 </test> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
108 </tests> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
109 <help> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
110 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
111 **Intro** |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
112 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
113 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
114 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
115 However, this Bowtie wrapper tool only takes FASTQ files as inputs. |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
116 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
117 Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1) |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
118 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
119 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
120 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
121 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
122 ------ |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
123 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
124 **What it does** |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
125 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
126 .. class:: infomark |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
127 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
128 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes. |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
129 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
130 Reads are Matched on DNA references as fast as possible, without taking care of mapping issues |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
131 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
132 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8* |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
133 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
134 unaligned reads at step N are used as input for sRbowtie at step N+1 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
135 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
136 ----- |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
137 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
138 **Input formats** |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
139 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
140 .. class:: warningmark |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
141 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
142 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter* |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
143 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
144 ----- |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
145 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
146 **OUTPUTS** |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
147 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
148 **Annotation table** |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
149 |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
150 </help> |
0528fced93a9
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff
changeset
|
151 </tool> |