Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

annotate readmap.xml @ 24:bf7388df53cf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 3effd45f45c37a6cdaf9b7b1da1ed4d10d3b0e38
author drosofff
date Sat, 08 Oct 2016 07:18:45 -0400
parents d6b93af0da55
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.2.0">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
2 <description>from sRbowtie aligment</description>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
3 <requirements>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
4 <requirement type="package" version="1.0.0">bowtie</requirement>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
5 <requirement type="package" version="0.9.0">pysam</requirement>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
6 <requirement type="package" version="1.9.3">numpy</requirement>
24
bf7388df53cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 3effd45f45c37a6cdaf9b7b1da1ed4d10d3b0e38
drosofff
parents: 23
diff changeset
7 <requirement type="package" version="1.3.0=r3.2.2_1">r-optparse</requirement>
bf7388df53cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 3effd45f45c37a6cdaf9b7b1da1ed4d10d3b0e38
drosofff
parents: 23
diff changeset
8 <requirement type="package" version="0.6_26=r3.2.2_2a">r-latticeextra</requirement>
bf7388df53cf planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 3effd45f45c37a6cdaf9b7b1da1ed4d10d3b0e38
drosofff
parents: 23
diff changeset
9 <requirement type="package" version="2.0.0=r3.2.2_0a">r-gridextra</requirement>
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
10 </requirements>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
11 <command><![CDATA[
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
12 python2 $__tool_directory__/readmap.py
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
13 #if $refGenomeSource.genomeSource == "history":
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
14 --reference_fasta
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
15 $refGenomeSource.ownFile ## index source
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
16 #else:
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
17 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
18 --reference_bowtie_index
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
19 $reference
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
20 #end if
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
21 --output_readmap
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
22 "$readmap_dataframe"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
23 --output_size_distribution
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
24 "$size_distribution_dataframe"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
25 --minquery $minquery
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
26 --maxquery $maxquery
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
27 --input
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
28 #for $i in $refGenomeSource.series
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
29 $i.input
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
30 #end for
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
31 --ext
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
32 #for $i in $refGenomeSource.series
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
33 $i.input.ext
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
34 #end for
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
35 --label
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
36 #for $i in $refGenomeSource.series
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
37 "$i.input.name"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
38 #end for
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
39 --normalization_factor
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
40 #for $i in $refGenomeSource.series
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
41 $i.norm
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
42 #end for
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
43 #if $gff:
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
44 --gff
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
45 $gff
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
46 #end if
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
47 ; Rscript $__tool_directory__/plot_size_readmap.r
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
48 --readmap_tab "$readmap_dataframe"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
49 --size_distribution_tab "$size_distribution_dataframe"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
50 --readmap_pdf "$readmap_PDF"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
51 --size_distribution_pdf "$size_PDF"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
52 --combi_pdf "$combi_PDF"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
53 --title "$title"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
54 --xlabel "$xlabel"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
55 --ylabel "$ylabel"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
56 --yrange "$yrange"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
57 --rows_per_page "$rows_per_page"
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
58 ]]>
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
59 </command>
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
60 <inputs>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
61 <conditional name="refGenomeSource">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
62 <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">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
63 <option value="indexed">Use a built-in index</option>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
64 <option value="history">Use one from the history</option>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
65 </param>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
66 <when value="indexed">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
67 <repeat name="series" title="Add alignment files">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
68 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
69 <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."/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
70 </param>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
71 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
72 </repeat>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
73 </when>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
74 <when value="history">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
75 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
76 <repeat name="series" title="Add alignment files">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
77 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
78 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
79 </repeat>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
80 </when>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
81 </conditional>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
82 <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"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
83 <!-- <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!"/> -->
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
84 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
85 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
86 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
87 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
88 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
89 <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
90 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
91 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
92 </param>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
93 </inputs>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
94 <outputs>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
95 <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
96 <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
97 <data format="pdf" name="readmap_PDF" label="Readmaps"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
98 <data format="pdf" name="size_PDF" label="Size distribution"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
99 <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
100 </outputs>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
101 <help>
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
102
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
103 **What it does**
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
104
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
105 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap",
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
106 where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
107 the number of reads per position. Reads that map in sense are on the top, reads that map antisense are on the bottom.
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
108
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
109
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
110 .. class:: warningmark
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
111
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
112 '''TIP''' The input data can be produced using the sRbowtie tool.
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
113
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
114 ----
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
115
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
116 '''Example'''
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
117
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
118 Query sequence::
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
119 For a SAM file as the following:
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
120
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
121 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
122
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
123 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
124
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
125 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
126
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
127 produce a plot like this:
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
128
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
129 ----
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
130
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
131 .. image:: static/images/readmap.png
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
132 :height: 800
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
133 :width: 500
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
134
23
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
135 </help>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
136 <tests>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
137 <test>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
138 <param name="genomeSource" value="history" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
139 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
140 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
141 <param name="series_0|norm" value="1" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
142 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
143 <param name="series_1|norm" value="1" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
144 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
145 <param name="series_2|norm" value="1" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
146 <param name="minquery" value="20" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
147 <param name="maxquery" value="30" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
148 <param name="title" value="Readmaps and size distributions" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
149 <param name="xlabel" value="Coordinates/read size" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
150 <param name="ylabel" value="Number of reads" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
151 <param name="rows_per_page" value="8" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
152 <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
153 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
154 </test>
d6b93af0da55 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6-dirty
mvdbeek
parents: 22
diff changeset
155 </tests>
0
9af9983dcd02 Imported from capsule None
drosofff
parents:
diff changeset
156 </tool>