small_rna_maps: small_rna_maps.xml annotate

annotate small_rna_maps.xml @ 14:cd75c72e1d75 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 5c55f75e094983228200111277fef7f349507174

author	artbio
date	Tue, 10 Apr 2018 10:13:04 -0400
parents	458a88317c22
children	82fedc576024

rev	line source
14 cd75c72e1d75 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 5c55f75e094983228200111277fef7f349507174 artbio parents: 13 diff changeset	1 <tool id="small_rna_maps" name="small_rna_maps" version="2.5.2">
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	2 <description></description>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	3 <requirements>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	10
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	11 </requirements>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	12 <stdio>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	13 <exit_code range="1:" level="fatal" description="Tool exception" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	14 </stdio>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	15 <command detect_errors="exit_code"><![CDATA[
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	16 #for $file in $series
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	17 samtools index '$file.inputs';
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	18 #end for
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	19 python '$__tool_directory__'/small_rna_maps.py
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	20 --inputs
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	21 #for $file in $series
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	22 '$file.inputs'
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	23 #end for
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	24 --sample_names
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	25 #for $sample in $series
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	26 '$sample.inputs.name'
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	27 #end for
8 1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	28 --minsize $minsize
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	29 --maxsize $maxsize
9 3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	30 --cluster $cluster
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	31 #if str($plots_options.plots_options_selector ) == "two_plot":
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	33 --outputs '$output_tab' '$extra_output_tab';
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	34 #elif str($plots_options.plots_options_selector ) == "global":
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	35 --plot_methods 'Size'
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	36 --outputs '$output_tab';
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	37 #else:
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	38 --plot_methods '${plots_options.first_plot}'
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	39 --outputs '$output_tab' ;
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	40 #end if
2 507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270 artbio parents: 1 diff changeset	41 Rscript '$__tool_directory__'/small_rna_maps.r
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270 artbio parents: 1 diff changeset	42 --first_dataframe '$output_tab'
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270 artbio parents: 1 diff changeset	43 --extra_dataframe '$extra_output_tab'
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	44 --normalization
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	45 #set $norm = ""
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	46 #for $file in $series
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	47 #set $norm += str($file.normalization)+' '
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	48 #end for
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	49 #set $norm = $norm[:-1]
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	50 '$norm'
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	51 #if $ylimits_cond.ylimits == "no":
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	52 --ymin '' --ymax ''
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	53 #else:
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	54 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	55 #end if
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	56 #if str($plots_options.plots_options_selector ) == "two_plot":
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	57 --first_plot_method '${plots_options.first_plot}'
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	58 --extra_plot_method '${plots_options.extra_plot}'
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	59 #elif str($plots_options.plots_options_selector ) == "global":
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	60 --first_plot_method 'Size'
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	61 --extra_plot_method ''
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	62 --global '${plots_options.mergestrands}'
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	63 #else:
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	64 --first_plot_method '${plots_options.first_plot}'
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	65 --extra_plot_method ''
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	66 #end if
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	67 --output_pdf '$output_pdf'
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	68 ]]></command>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	69 <inputs>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	70 <repeat name="series" title="Input" min="1">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	71 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	72 help="If 'multiple datasets' method is used, the same normalization factor will be applied to each dataset. Please refer to the help section for more information." />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	73 <param name="normalization" type="float" label="Enter a size/normalization factor."
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	74 help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	75 </repeat>
8 1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	76 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	77 value="0" help="default value: 0" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	78 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	79 value="10000" help="default value: 10000" />
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	80 <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	81 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	82 <conditional name="plots_options">
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	83 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	84 <option value="one_plot">Just one plot per chromosome</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	85 <option value="two_plot" selected="True">Two plots per chromosome</option>
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	86 <option value="global">Global read size distributions of aligned reads</option>
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	87 </param>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	88 <when value="two_plot">
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	89 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	90 <option value="Counts">Counts</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	91 <option value="Coverage">Coverage</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	92 <option value="Mean">Mean Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	93 <option value="Median">Median Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	94 <option value="Size">Size Distributions</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	95 </param>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	96 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	97 <option value="Counts">Counts</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	98 <option value="Coverage">Coverage</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	99 <option value="Mean">Mean Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	100 <option value="Median">Median Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	101 <option value="Size">Size Distributions</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	102 </param>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	103 </when>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	104 <when value="one_plot">
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	105 <param name="first_plot" type="select" display="radio" label="select the type of plot">
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	106 <option value="Counts">Counts</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	107 <option value="Coverage">Coverage</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	108 <option value="Mean">Mean Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	109 <option value="Median">Median Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	110 <option value="Size">Size Distributions</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	111 </param>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	112 </when>
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	113 <when value="global">
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	114 <param name="first_plot" type="hidden" value="Size"/>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	115 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	116 <option value="nomerge">Do not merge</option>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	117 <option value="merge">Merge forward and reverse reads</option>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	118 </param>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	119 </when>
5 12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449 artbio parents: 4 diff changeset	120 </conditional>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	121 <conditional name="ylimits_cond">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	122 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	123 help="This limit won't be applied to size distribution plots"/>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	124 <when value="yes">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	125 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	126 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	127 </when>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	128 <when value="no">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	129 </when>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	130 </conditional>
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	131 </inputs>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	132
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	133 <outputs>
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	134 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	135 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	136 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	137 </data>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	138 <data format="pdf" name="output_pdf" label="small RNA maps" />
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	139 </outputs>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	140
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	141 <tests>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	142 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	143 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	144 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	145 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	146 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	147 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	148 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	149 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	150 <param name="ylimits" value="yes" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	151 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	152 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	153 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	154 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	155 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	156 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	157 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	158 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	159 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	160 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	161 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	162 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	163 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	164 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	165 <param name="cluster" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	166 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	167 <param name="first_plot" value="Coverage" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	168 <output file="input1_coverage_cluster5.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	169 <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	170 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	171 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	172 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	173 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	174 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	175 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	176 <param name="minsize" value="20" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	177 <param name="maxsize" value="30" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	178 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	179 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	180 <param name="first_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	181 <output file="input1_min20_max30_size.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	182 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	183 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	184 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	185 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	186 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	187 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	188 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	189 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	190 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	191 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	192 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	193 <param name="first_plot" value="Mean" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	194 <output file="input1_mean.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	195 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	196 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	197 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	198 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	199 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	200 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	201 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	202 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	203 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	204 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	205 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	206 <param name="first_plot" value="Median" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	207 <output file="input1_median.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	208 <output file="input1_single_plot_median.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	209 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	210 <test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	211 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	212 <param name="inputs" value="input1.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	213 <param name="normalization" value="1.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	214 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	215 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	216 <param name="inputs" value="input2.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	217 <param name="normalization" value="2.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	218 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	219 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	220 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	221 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	222 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	223 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	224 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	225 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	226 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	227 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	228 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	229 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	230 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	231 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	232 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	233 <param name="inputs" value="input2.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	234 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	235 </repeat>
8 1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	236 <param name="minsize" value="0" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	237 <param name="maxsize" value="10000" />
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	238 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	239 <param name="ylimits" value="yes" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	240 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	241 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	242 <param name="plots_options_selector" value="two_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	243 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	244 <param name="extra_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	245 <output file="input1_input2_counts.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	246 <output file="input1_input2_size.tab" name="extra_output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	247 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	248 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	249 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	250 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	251 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	252 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	253 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	254 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	255 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	256 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	257 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	258 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	259 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	260 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	261 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	262 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	263 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	264 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	265 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	266 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	267 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	268 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	269 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	270 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	271 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	272 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	273 </repeat>
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	274 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	275 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	276 <param name="cluster" value="0" />
9 3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	277 <param name="plots_options_selector" value="one_plot" />
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	278 <param name="first_plot" value="Coverage" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	279 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	280 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
9 3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	281 </test>
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	282 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	283 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	284 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	285 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	286 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	287 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	288 <param name="inputs" value="input2.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	289 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	290 </repeat>
9 3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	291 <param name="minsize" value="0" />
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	292 <param name="maxsize" value="10000" />
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	293 <param name="cluster" value="0" />
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	294 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	295 <param name="mergestrands" value="nomerge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	296 <param name="first_plot" value="Size" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	297 <output file="size.tab" name="output_tab" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	298 <output file="global_nomerge.pdf" name="output_pdf" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	299 </test>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	300 <test>
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	301 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	302 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	303 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	304 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	305 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	306 <param name="inputs" value="input2.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	307 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	308 </repeat>
8 1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	309 <param name="minsize" value="0" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60 artbio parents: 7 diff changeset	310 <param name="maxsize" value="10000" />
9 3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5 artbio parents: 8 diff changeset	311 <param name="cluster" value="0" />
7 a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	312 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	313 <param name="mergestrands" value="merge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	314 <param name="first_plot" value="Size" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	315 <output file="size.tab" name="output_tab" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	316 <output file="global_merge.pdf" name="output_pdf" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f artbio parents: 6 diff changeset	317 </test>
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	318 </tests>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	319 <help>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	320
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	321 What it does
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	322
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	323 Plots mapping statistics of an alignment along the reference chromosomes :
6 a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d artbio parents: 5 diff changeset	324
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	325 - counts
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	326 - mean sizes
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	327 - median sizes
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	328 - coverage depth
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	329 - size distribution
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	330
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	331 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	332 in each position of a chromosome reference.
6 a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d artbio parents: 5 diff changeset	333 Coverage depths are computed from the input bam alignment files using the python pysam module.
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	334
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	335 The metrics mentioned above can be plotted either separately:
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	336
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	337 .. image:: one_plot.png
6 a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d artbio parents: 5 diff changeset	338
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	339 Or in all possible pairwise combinations:
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	340
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	341 .. image:: two_plot.png
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	342
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	343 For comparison purposes, values from bam alignment files can be normalized by a size factor
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	344 before plotting.
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	345
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	346 Inputs
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	347
2 507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270 artbio parents: 1 diff changeset	348 bam alignment files that must be
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	349
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	350 - single-read
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	351 - sorted
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	352 - mapped to the same reference
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	353
13 458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	354 To plot 2 alignment files in the same PDF output the 'single dataset' method should be used.
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	355
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	356 .. class:: warningmark
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	357
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	358 If the 'multiple dataset' method is used the normalization factor will be applied to every file selected in the input list.
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	359 Additionally each file in the selected list will be plotted in a separate PDF file.
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b artbio parents: 12 diff changeset	360
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	361 Output
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	362
12 d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f artbio parents: 11 diff changeset	363 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
0 6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	364
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	365 </help>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	366
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	367 <citations>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	368 <citation type="doi">10.1093/bioinformatics/btp352</citation>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	369 <citation type="bibtex">@Book{,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	370 title = {Lattice: Multivariate Data Visualization with R},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	371 author = {Deepayan Sarkar},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	372 publisher = {Springer},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	373 address = {New York},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	374 year = {2008},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	375 note = {ISBN 978-0-387-75968-5},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	376 url = {http://lmdvr.r-forge.r-project.org},
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	377 }</citation>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	378 </citations>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	379 </tool>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959 artbio parents: diff changeset	380

Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 14:cd75c72e1d75 draft