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comparison ideas.xml @ 26:53891e4e4c63 draft

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Uploaded
author greg
date Mon, 14 Aug 2017 08:31:13 -0400
parents 0169856fe7bb
children 0cf199863400
comparison
equal deleted inserted replaced
25:0169856fe7bb 26:53891e4e4c63
55 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets 55 #set standardize_datasets = $standardize_datasets_cond.standardize_datasets
56 #if str($standardize_datasets) == 'yes': 56 #if str($standardize_datasets) == 'yes':
57 -norm 57 -norm
58 #end if 58 #end if
59 ############################################## 59 ##############################################
60 ## Conform the prepMat config output to the
61 ## format expected by the R matrix builder.
62 ##############################################
63 && cut -d' ' $prep_input_config -f1,2 > file1.txt
64 && ls -p tmp/ | grep ".bed.gz" > file2.txt
65 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
66 ##############################################
60 ## Build the R matrix from the prepMat output 67 ## Build the R matrix from the prepMat output
61 ############################################## 68 ##############################################
62 ##&& Rscript '$__tool_directory__/build_matrix.R' 69 ##&& Rscript '$__tool_directory__/build_matrix.R'
63 ##-i $tmp_dir/*.bed.gz 70 ##-i $tmp_dir/*.bed.gz
64 ##-o $ideas_matrix_input_file 71 ##-o $ideas_matrix_input_file
65 ##-w $ideas_input_dir 72 ##-w $ideas_input_dir
66 && cut -d' ' $prep_input_config -f1,2 > file1.txt
67 && ls -p tmp/ | grep ".bed.gz" > file2.txt
68 && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config
69 ############################################## 73 ##############################################
70 ## Run IDEAS on the R matrix 74 ## Run IDEAS on the R matrix
71 ############################################## 75 ##############################################
72 && ideas 76 && ideas
73 '$prep_output_config' 77 '$prep_output_config'
78 $tmp_dir/*.bed
74 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 79 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
75 #if str($smoother_annotation) == 'yes': 80 #if str($smoother_annotation) == 'yes':
76 -hp 81 -hp
77 #end if 82 #end if
78 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation 83 #set smoother_annotation = $smoother_annotation_cond.smoother_annotation
120 #if str($set_max_standard_dev) == 'yes': 125 #if str($set_max_standard_dev) == 'yes':
121 -maxerr $set_max_standard_dev_cond.max_standard_dev 126 -maxerr $set_max_standard_dev_cond.max_standard_dev
122 #end if 127 #end if
123 -thread \${GALAXY_SLOTS:-4} 128 -thread \${GALAXY_SLOTS:-4}
124 -o $prep_output_dir 129 -o $prep_output_dir
130 && mv $prep_output_dir/*cluster $output_cluster
131 && mv $prep_output_dir/*.para $output_para
132 && mv $prep_output_dir/*.profile $output_profile
125 && mv $prep_output_dir/*.state $output_state 133 && mv $prep_output_dir/*.state $output_state
126 && mv $prep_output_dir/*.para $output_para
127 && mv $prep_output_dir/*cluster $output_cluster
128 ]]></command> 134 ]]></command>
129 <configfiles> 135 <configfiles>
130 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat: 136 <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat:
131 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} 137 ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input}
132 #end for ]]></configfile> 138 #end for ]]></configfile>
282 <param name="max_standard_dev" type="float" value="100000000" label="Maximum standard deviation for the emission Gaussian distribution"/> 288 <param name="max_standard_dev" type="float" value="100000000" label="Maximum standard deviation for the emission Gaussian distribution"/>
283 </when> 289 </when>
284 </conditional> 290 </conditional>
285 </inputs> 291 </inputs>
286 <outputs> 292 <outputs>
293 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
294 <data name="output_para" format="tabular" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>
295 <data name="output_profile" format="txt" label="${tool.name} (profile) on ${on_string}"/>
287 <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/> 296 <data name="output_state" format="txt" label="${tool.name} (epigenetic states and position classes) on ${on_string}"/>
288 <data name="output_para" format="txt" label="${tool.name} (epigenetic state frequency, mean and variance parameters) on ${on_string}"/>
289 <data name="output_cluster" format="txt" label="${tool.name} (local cell type clustering) on ${on_string}"/>
290 </outputs> 297 </outputs>
291 <tests> 298 <tests>
292 </tests> 299 </tests>
293 <help> 300 <help>
294 **What it does** 301 **What it does**