Mercurial > repos > artbio > small_read_size_histograms

annotate size_histogram.xml @ 1:cfa459481913 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/small_read_size_histograms commit 87fad8a906abdb9dc2ecaa2457fb26ab2b09895d
author artbio
date Tue, 11 Jul 2017 13:09:35 -0400
parents 439113f55798
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
1 <tool id="artbio_size_histogram" name="Generate read size histograms" version="1.0.0">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
2 <description>from alignment files</description>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
3 <requirements>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
4 <requirement type="package" version="1.2.0=py27_0">bowtie</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
6 <requirement type="package" version="1.9.3">numpy</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
7 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
8 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
9 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
10 </requirements>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
12 python '$__tool_directory__'/size_histogram.py
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
13 #if $refGenomeSource.genomeSource == "history":
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
14 --reference_fasta ## sys.argv[2]
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
15 '$refGenomeSource.ownFile' ## index source
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
16 #else:
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
17 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
18 --reference_bowtie_index
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
19 '$reference'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
20 #end if
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
21 --output_size_distribution
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
22 '$size_distribution_dataframe'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
23 --minquery
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
24 $minquery
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
25 --maxquery
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
26 $maxquery
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
27 --input
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
28 #for $i in $refGenomeSource.series
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
29 '$i.input'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
30 #end for
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
31 --ext
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
32 #for $i in $refGenomeSource.series
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
33 '$i.input.ext'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
34 #end for
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
35 --label
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
36 #for $i in $refGenomeSource.series
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
37 "$i.input.element_identifier"
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
38 #end for
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
39 #if $gff:
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
40 --gff '$gff'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
41 #end if
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
42 #if $global.value == 'yes':
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
43 --global_size
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
44 #end if
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
45 #if $collapsestrands.value == 'yes':
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
46 --collapse
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
47 #end if
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
48 --normalization_factor
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
49 #for $i in $refGenomeSource.series
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
50 $i.norm
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
51 #end for
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
52 &&
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
53 Rscript '$__tool_directory__'/size_histogram.r
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
54 --global '$global'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
55 --size_distribution_tab '$size_distribution_dataframe'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
56 --size_distribution_pdf '$size_PDF'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
57 --title '$title'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
58 --ylabel '$ylabel'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
59 --yrange '$yrange'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
60 --rows_per_page '$rows_per_page'
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
61 ]]></command>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
62 <inputs>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
63 <conditional name="refGenomeSource">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
64 <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">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
65 <option value="indexed">Use a built-in index</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
66 <option value="history">Use one from the history</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
67 </param>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
68 <when value="indexed">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
69 <repeat name="series" title="Add alignment files">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
70 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
71 <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."/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
72 </param>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
73 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
74 </repeat>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
75 </when>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
76 <when value="history">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
77 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
78 <repeat name="series" title="Add alignment files">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
79 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
80 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
81 </repeat>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
82 </when>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
83 </conditional>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
84 <param name="gff" type="data" format="gff,gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
85 <!-- <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!"/> -->
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
86 <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
87 <option value="no">for each item</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
88 <option value="yes">global</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
89 </param>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
90 <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
91 <option value="no">Do not collapse</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
92 <option value="yes">Collapse + and - reads</option>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
93 </param>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
94 <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
95 <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
96 <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
97 <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
98 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
99 <param name="yrange" type="integer" size="3" value="0" label="y axis range for size distributions. 0 means auto-scaling."/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
100 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
101 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
102 </param>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
103 </inputs>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
104
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
105 <outputs>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
106 <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
107 <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
108 </outputs>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
109
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
110 <help>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
111
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
112 **What it does**
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
113
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
114 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes,
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
115 where by default for each "chromosome" a histogram of read sizes is drawn.
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
116 Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
117
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
118
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
119 .. class:: warningmark
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
120
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
121 '''TIP''' The input data can be produced using the sRbowtie tool.
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
122
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
123 ----
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
124
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
125 '''Example'''
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
126
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
127 Query sequence::
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
128 For a SAM file as the following:
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
129
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
130 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
131
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
132 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
133
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
134 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
135
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
136 produce a plot like this:
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
137
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
138 ----
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
139
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
140 .. image:: static/images/size_histogram.png
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
141 :height: 800
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
142 :width: 500
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
143
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
144 </help>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
145 <tests>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
146 <test>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
147 <param name="genomeSource" value="history" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
148 <param name="ownFile" value="transposons.fasta" ftype="fasta" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
149 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
150 <param name="series_0|norm" value="1" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
151 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
152 <param name="series_1|norm" value="1" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
153 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
154 <param name="series_2|norm" value="1" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
155 <param name="global" value="no" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
156 <param name="collapsestrands" value="no" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
157 <param name="minquery" value="18"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
158 <param name="maxquery" value="30"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
159 <param name="title" value="Size distribution"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
160 <param name="xlabel" value="Size in nucleotides"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
161 <param name="ylabel" value="Number of reads"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
162 <param name="rows_per_page" value="10"/>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
163 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
164 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
165 </test>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
166 </tests>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
167 </tool>
439113f55798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_read_size_histograms commit ab983b2e57321e8913bd4d5f8fc89c3223c69869
artbio
parents:
diff changeset
168