annotate readmap.xml @ 4:4efe210c91f3 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
author mvdbeek
date Wed, 03 Feb 2016 11:35:00 -0500
parents ebfc73c72652
children 68f58363f1c6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4efe210c91f3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
mvdbeek
parents: 2
diff changeset
1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.3">
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
2 <description>from sRbowtie aligment</description>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
3 <requirements>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
4 <requirement type="package" version="0.12.7">bowtie</requirement>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
5 <requirement type="package" version="0.7.7">pysam</requirement>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
6 <requirement type="package" version="3.1.2">R</requirement>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
7 <requirement type="package" version="2.14">biocbasics</requirement>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
8 <requirement type="package" version="1.9">numpy</requirement>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
9 </requirements>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
10 <command interpreter="python">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
11 readmap.py
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
12 #if $refGenomeSource.genomeSource == "history":
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
13 --reference_fasta ## sys.argv[2]
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
14 $refGenomeSource.ownFile ## index source
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
15 #else:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
16 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
17 --reference_bowtie_index
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
18 $reference
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
19 #end if
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
20 --rcode
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
21 $plotCode
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
22 --output_readmap
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
23 $readmap_dataframe
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
24 --output_size_distribution
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
25 $size_distribution_dataframe
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
26 --minquery
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
27 $minquery
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
28 --maxquery
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
29 $maxquery
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
30 --input
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
31 #for $i in $refGenomeSource.series
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
32 $i.input
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
33 #end for
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
34 --ext
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
35 #for $i in $refGenomeSource.series
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
36 $i.input.ext
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
37 #end for
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
38 --label
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
39 #for $i in $refGenomeSource.series
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
40 "$i.input.name"
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
41 #end for
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
42 --normalization_factor
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
43 #for $i in $refGenomeSource.series
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
44 $i.norm
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
45 #end for
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
46 #if $gff:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
47 --gff
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
48 $gff
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
49 #end if
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
50
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
51 </command>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
52 <inputs>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
53 <conditional name="refGenomeSource">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
54 <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">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
55 <option value="indexed">Use a built-in index</option>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
56 <option value="history">Use one from the history</option>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
57 </param>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
58 <when value="indexed">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
59 <repeat name="series" title="Add alignment files">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
60 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
61 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
62 </param>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
63 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
64 </repeat>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
65 </when>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
66 <when value="history">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
67 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
68 <repeat name="series" title="Add alignment files">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
69 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
70 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
71 </repeat>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
72 </when>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
73 </conditional>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
74 <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
75 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
80 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
2
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
81 <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/>
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
82 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
83 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
84 </param>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
85 </inputs>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
86 <configfiles>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
87 <configfile name="plotCode">
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
88 ## Setup R error handling to go to stderr
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
89 options( show.error.messages=F,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
90 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
91 library(RColorBrewer)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
92 library(lattice)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
93 library(latticeExtra)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
94 library(grid)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
95 library(gridExtra)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
96
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
97 ## data frames implementation
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
98
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
99 rm=read.delim("${readmap_dataframe}", header=T, row.names=NULL)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
100 n_samples=length(unique(rm\$sample))
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
101 genes=unique(levels(rm\$gene))
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
102 per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) ####### ?
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
103 n_genes=length(per_gene_readmap)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
104
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
105 size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
106 per_gene_size=lapply(genes, function(x) subset(size, gene==x)) ###### ?
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
107
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
108 ## end of data frames implementation
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
109
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
110 ## functions
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
111
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
112 plot_readmap=function(df, ...) {
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
113 combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
114 data=df,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
115 type='h',
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
116 scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
117 xlab=NULL, main=NULL, ylab=NULL,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
118 as.table=T,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
119 origin = 0,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
120 horizontal=FALSE,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
121 group=polarity,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
122 col=c("red","blue"),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
123 par.strip.text = list(cex=0.7),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
124 ...))
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
125 }
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
126
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
127 plot_size_distribution= function(df, ...) {
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
128 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
129 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
130 horizontal=FALSE,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
131 group=polarity,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
132 stack=TRUE,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
133 col=c('red', 'blue'),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
134 cex=0.75,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
135 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
136 prepanel=smR.prepanel,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
137 xlab = NULL,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
138 ylab = NULL,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
139 main = NULL,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
140 as.table=TRUE,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
141 newpage = T,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
142 par.strip.text = list(cex=0.7),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
143 ...)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
144 combineLimits(bc)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
145 }
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
146
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
147 ## end of functions
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
148
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
149 ## function parameters'
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
150
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
151 par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
152 par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
153 par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
154 par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
155
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
156 ## end of function parameters'
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
157
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
158 ## GRAPHS
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
159
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else {
1
e4874d1ae69d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 450d1b3d954cc7d96e53652d468811546951f995
drosofff
parents: 0
diff changeset
161 rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 }
e4874d1ae69d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 450d1b3d954cc7d96e53652d468811546951f995
drosofff
parents: 0
diff changeset
162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 }
e4874d1ae69d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 450d1b3d954cc7d96e53652d468811546951f995
drosofff
parents: 0
diff changeset
163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 }
e4874d1ae69d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 450d1b3d954cc7d96e53652d468811546951f995
drosofff
parents: 0
diff changeset
164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
165
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
166 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
167 for (i in seq(1,n_genes,rows_per_page)) {
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
168 start=i
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
169 end=i+rows_per_page-1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
170 if (end>n_genes) {end=n_genes}
2
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
171 if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
172 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) }
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
173 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
174 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
175 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
176 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
177 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
178 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
179 do.call(grid.arrange, args.list)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
180 }
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
181 devname=dev.off()
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
182
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
183
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
184 pdf(file="${size_PDF}", paper="special", height=page_height_simple, width=page_width)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
185 for (i in seq(1,n_genes,rows_per_page)) {
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
186 start=i
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
187 end=i+rows_per_page-1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
188 if (end>n_genes) {end=n_genes}
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
189 plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
190 args.list=c(plot.list, list(nrow=rows_per_page, ncol=1,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
191 main=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
192 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
193 #sub="readsize in nucleotides"
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
194 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
195 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
196 do.call(grid.arrange, args.list)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
197 }
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
198 devname=dev.off()
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
199
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
200 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
201 for (i in seq(1,n_genes,rows_per_page/2)) {
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
202 start=i
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
203 end=i+rows_per_page/2-1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
204 if (end>n_genes) {end=n_genes}
2
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
205 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
206 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
207 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
2
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
parents: 1
diff changeset
208 plot.list=rbind(readmap_plot.list, size_plot.list )
0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
209 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
210 main=textGrob("${title}", gp=gpar(cex=1), just="top"),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
211 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
212 sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
213 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
214 )
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
215 do.call(grid.arrange, args.list)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
216 }
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
217 devname=dev.off()
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
218
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
219
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
220 </configfile>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
221 </configfiles>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
222
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
223 <outputs>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
224 <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
225 <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
226 <data format="pdf" name="readmap_PDF" label="Readmaps"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
227 <data format="pdf" name="size_PDF" label="Size distribution"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
228 <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
229 </outputs>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
230 <help>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
231
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
232 **What it does**
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
233
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
234 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap",
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
235 where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
236 the number of reads per position. Reads that map in sense are on the top, reads that map antisense are on the bottom.
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
237
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
238
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
239 .. class:: warningmark
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
240
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
241 '''TIP''' The input data can be produced using the sRbowtie tool.
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
242
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
243 ----
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
244
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
245 '''Example'''
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
246
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
247 Query sequence::
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
248 For a SAM file as the following:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
249
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
250 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
251
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
252 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
253
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
254 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
255
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
256 produce a plot like this:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
257
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
258 ----
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
259
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
260 .. image:: static/images/readmap.png
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
261 :height: 800
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
262 :width: 500
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
263
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
264 </help>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
265 <tests>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
266 <test>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
267 <param name="genomeSource" value="history" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
268 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
269 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
270 <param name="series_0|norm" value="1" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
271 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
272 <param name="series_1|norm" value="1" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
273 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
274 <param name="series_2|norm" value="1" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
275 <param name="minquery" value="20" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
276 <param name="maxquery" value="30" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
277 <param name="title" value="Readmaps and size distributions" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
278 <param name="xlabel" value="Coordinates/read size" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
279 <param name="ylabel" value="Number of reads" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
280 <param name="rows_per_page" value="8" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
281 <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
282 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
283 <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
284 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
285 <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" />
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
286 </test>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
287 </tests>
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
288 </tool>