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comparison ideas.xml @ 106:a0e38f759ad5 draft

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author greg
date Tue, 14 Nov 2017 10:34:55 -0500
parents 4e3a891ca4d8
children 278abbd4399c
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105:14659ab1e709 106:a0e38f759ad5
4 <requirement type="package" version="2.26.0">bedtools</requirement> 4 <requirement type="package" version="2.26.0">bedtools</requirement>
5 <requirement type="package" version="332">ucsc-bedgraphtobigwig</requirement> 5 <requirement type="package" version="332">ucsc-bedgraphtobigwig</requirement>
6 <requirement type="package" version="332">ucsc-bedsort</requirement> 6 <requirement type="package" version="332">ucsc-bedsort</requirement>
7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement> 7 <requirement type="package" version="332">ucsc-bigwigaverageoverbed</requirement>
8 <requirement type="package" version="1.20">ideas</requirement> 8 <requirement type="package" version="1.20">ideas</requirement>
9 <requirement type="package" version="1.3.2">r-optparse</requirement> 9 <requirement type="package" version="1.4.4">r-optparse</requirement>
10 </requirements> 10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #set output_dir = "output_dir" 12 #set output_dir = "output_dir"
13 #set tmp_dir = "tmp" 13 #set tmp_dir = "tmp"
14 #set prep_input_config = "prep_input_config.txt" 14 #set prep_input_config = "prep_input_config.txt"
15 #set prep_output_config = "prep_output_config.txt" 15 #set prep_output_config = "prep_output_config.txt"
16 ############################################## 16 ##############################################
17 ## Create the config file and prepare the data 17 ## Create the config file and prepare the data
18 ############################################## 18 ##############################################
19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window 19 #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window
20 mkdir $output_dir && 20 mkdir '$output_dir' &&
21 cp '$gen_prep_input_config' $prep_input_config && 21 cp '$gen_prep_input_config' $prep_input_config &&
22 prepMat 22 prepMat
23 $prep_input_config 23 $prep_input_config
24 #if str($specify_genomic_window) == "yes": 24 #if str($specify_genomic_window) == "yes":
25 -bed '$specify_genomic_window_cond.bed_input' 25 -bed '$specify_genomic_window_cond.bed_input'
95 #end if 95 #end if
96 && mv ./*.cluster '$output_dir' 96 && mv ./*.cluster '$output_dir'
97 && mv ./*.para '$output_dir' 97 && mv ./*.para '$output_dir'
98 && mv ./*.profile '$output_dir' 98 && mv ./*.profile '$output_dir'
99 && mv ./*.state '$output_dir' 99 && mv ./*.state '$output_dir'
100 && Rscript '$__tool_directory__/create_heatmap.R'
101 -i '$output_dir/*.para'
102 -o '$output_heatmap'
100 ]]></command> 103 ]]></command>
101 <configfiles> 104 <configfiles>
102 <configfile name="gen_prep_input_config"><![CDATA[#import os 105 <configfile name="gen_prep_input_config"><![CDATA[#if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
103 #if str($cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor) == "extract":
104 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions 106 #set input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions
105 #for $i in $cell_type_epigenetic_factor_cond.input: 107 #for $i in $cell_type_epigenetic_factor_cond.input:
106 #set file_name_with_ext = $i.name 108 #set file_name_with_ext = $i.name
107 #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext 109 #assert str($file_name_with_ext).find("-") >= 0, "The selected input '%s' is invalid because it does not include the '-' character which is required when setting cell type and epigenetic factor names by extracting them from the input file names." % $file_name_with_ext
108 #set file_name = $file_name_with_ext.split(".")[0] 110 #set file_name = $file_name_with_ext.split(".")[0]
202 </inputs> 204 </inputs>
203 <outputs> 205 <outputs>
204 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}"> 206 <data name="output_log" format="txt" label="${tool.name} (output log) on ${on_string}">
205 <filter>save_ideas_log == 'yes'</filter> 207 <filter>save_ideas_log == 'yes'</filter>
206 </data> 208 </data>
209 <data name="output_heatmap" format="pdf" label="${tool.name} (heatmap) on ${on_string}"/>
207 <collection name="output" type="list"> 210 <collection name="output" type="list">
208 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/> 211 <discover_datasets pattern="__name__" directory="output_dir" format="txt"/>
209 </collection> 212 </collection>
210 </outputs> 213 </outputs>
211 <tests> 214 <tests>
222 <output_collection name="primary_fna" type="list"> 225 <output_collection name="primary_fna" type="list">
223 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/> 226 <element name="3722.fna.aln" file="3722.fna.aln" ftype="fasta"/>
224 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/> 227 <element name="38889.fna.aln" file="38889.fna.aln" ftype="fasta"/>
225 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/> 228 <element name="39614.fna.aln" file="39614.fna.aln" ftype="fasta"/>
226 </output_collection> 229 </output_collection>
227
228 </test> 230 </test>
229 <test> 231 <test>
230 <param name="cell_type_epigenetic_factor" value="manual"/> 232 <param name="cell_type_epigenetic_factor" value="manual"/>
231 <repeat name="input_repeat"> 233 <repeat name="input_repeat">
232 <param name="cell_type_name" value="e001" /> 234 <param name="cell_type_name" value="e001" />