Mercurial > repos > greg > ideas
diff ideas.xml @ 65:e29e083ebef7 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 24 Aug 2017 07:57:30 -0400 |
| parents | 19112fe6e5bd |
| children | dc5d5a08c370 |
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--- a/ideas.xml Thu Aug 24 07:54:16 2017 -0400 +++ b/ideas.xml Thu Aug 24 07:57:30 2017 -0400 @@ -9,27 +9,29 @@ <requirement type="package" version="1.3.2">r-optparse</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ -#set tmp_dir = "tmp" -#set prep_output_config = "prep_output_config.txt" +#import os +#set tmp_dir = 'tmp' +#set prep_output_config = 'prep_output_config.txt' +##set ideas_input_dir = 'ideas_input' +##set ideas_matrix_input_file = $os.path.join($ideas_input_dir, 'r_matrix.txt') +##mkdir -p $ideas_input_dir && ############################################## ## Create the config file and prepare the data ############################################## #set input_type = $input_type_cond.input_type -#if str($input_type) == "datasets": - #set cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond - #set cell_type_epigenetic_factor = $cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor +cp '$prep_input_config' 'prep_input_config.txt' && +prepMat +#if str($input_type) == 'datasets': + '$prep_input_config' #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window - cp '$gen_prep_input_config' "prep_input_config.txt" && - prepMat - '$gen_prep_input_config' - #if str($specify_genomic_window) == "yes": + #if str($specify_genomic_window) == 'yes': -bed '$specify_genomic_window_cond.bed_input' #else: -gsz '$chromInfo' -wsz $specify_genomic_window_cond.window_size #set restrict_chromosomes = $specify_genomic_window_cond.restrict_chromosomes_cond.restrict_chromosomes - #if str($restrict_chromosomes) == "yes": + #if str($restrict_chromosomes) == 'yes': #set chroms = [] #set chrom_repeat = $specify_genomic_window_cond.restrict_chromosomes_cond.chrom_repeat #for $i in $chrom_repeat.chrom @@ -41,7 +43,7 @@ #end if $bychr -c $reads_per_bp -#if str($blacklist_input) not in ["None", ""]: +#if str($blacklist_input) not in ['None', '']: -exclude '$blacklist_input' #end if $norm @@ -49,7 +51,7 @@ ## Coerce the prepMat config output to the ## format expected by the R matrix builder. ############################################## -&& cut -d' ' '$gen_prep_input_config' -f1,2 > file1.txt +&& cut -d' ' $prep_input_config -f1,2 > file1.txt && ls tmp/*.bed.gz > file2.txt && paste <(cat file1.txt) <(cat file2.txt) > $prep_output_config ############################################## @@ -64,10 +66,10 @@ ############################################## && ideas '$prep_output_config' -#if str($input_type) == "datasets": +#if str($input_type) == 'datasets': #set specify_genomic_window_cond = $input_type_cond.specify_genomic_window_cond #set specify_genomic_window = $specify_genomic_window_cond.specify_genomic_window - #if str($specify_genomic_window) == "yes": + #if str($specify_genomic_window) == 'yes': '$specify_genomic_window_cond.bed_input' #else: $tmp_dir/*.bed @@ -76,29 +78,29 @@ $tmp_dir/*.bed #end if $hp -#if str($log2) != "0.0": +#if str($log2) != '0.0': -log2 $log2 #end if -#if str($max_states) != "0.0": +#if str($max_states) != '0.0': -G $max_states #end if -#if str($initial_states) != "0": +#if str($initial_states) != '0': -C $initial_states #end if -#if str($max_position_classes) != "0": +#if str($max_position_classes) != '0': -P $max_position_classes #end if -#if str($max_cell_type_clusters) != "0": +#if str($max_cell_type_clusters) != '0': -K $max_cell_type_clusters #end if -#if str($prior_concentration) != "0.0": +#if str($prior_concentration) != '0.0': -A $prior_concentration #end if -sample $burnin_num $mcmc_num -#if str($minerr) != "0.0": +#if str($minerr) != '0.0': -minerr $minerr #end if -#if str($maxerr) != "0.0": +#if str($maxerr) != '0.0': -maxerr $maxerr #end if -thread \${GALAXY_SLOTS:-4} @@ -109,28 +111,9 @@ && mv ./*.state $output_state ]]></command> <configfiles> - <configfile name="gen_prep_input_config"><![CDATA[ -#import os -#if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "manual": - #for $input_items in $input_type_cond.cell_type_epigenetic_factor_cond.input_repeat: + <configfile name="prep_input_config"><![CDATA[#for $input_items in $input_type_cond.input_repeat: ${input_items.cell_type_name} ${input_items.epigenetic_factor_name} ${input_items.input} - #end for -#else if $input_type_cond.cell_type_epigenetic_factor_cond.cell_type_epigenetic_factor == "extract": - #set $cell_type_epigenetic_factor_cond = $input_type_cond.cell_type_epigenetic_factor_cond - #set $input_name_positions = $cell_type_epigenetic_factor_cond.input_name_positions - #for $i in $cell_type_epigenetic_factor_cond.input: - #set $file_name_with_ext = $os.path.basename($i) - #set $file_name = $file_name_with_ext.split(".")[0] - #if $input_name_positions == "cell_first": - #set $cell_type_name = $file_name.split("-")[0] - #set $epigenetic_factor_name = $file_name.split("-")[1] - #else: - #set $cell_type_name = $file_name.split("-")[1] - #set $epigenetic_factor_name = $file_name.split("-")[0] - #end if -${cell_type_name} ${epigenetic_factor_name} ${i} - #end for -#end if]]></configfile> +#end for ]]></configfile> </configfiles> <inputs> <conditional name="input_type_cond"> @@ -139,36 +122,18 @@ <option value="data_matrix">Data matrix</option> </param> <when value="datasets"> - <conditional name="cell_type_epigenetic_factor_cond"> - <param name="cell_type_epigenetic_factor" type="select" label="Set cell type and epigenetic factor names by"> - <option value="extract" selected="true">extracting them from the selected input file names</option> - <option value="manual">manually setting them for each selected input</option> + <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1"> + <param name="cell_type_name" type="text" value="" label="Cell type name"> + <validator type="empty_field"/> </param> - <when value="extract"> - <param name="input" type="data" format="bigwig,bam" multiple="True" label="BAM or BigWig file"> - <validator type="empty_field"/> - <validator type="unspecified_build"/> - </param> - <param name="input_name_positions" type="select" display="radio" label="Selected input file name pattern is" help="A '-' character must separate cell type and epigenetic factor names within the selected input file names"> - <option value="cell_first" selected="true">Cell type name - Epigenetic factor name</option> - <option value="cell_last">Epigenetic factor name - Cell type name</option> - </param> - </when> - <when value="manual"> - <repeat name="input_repeat" title="Cell type, Epigenetic factor and Input" min="1"> - <param name="cell_type_name" type="text" value="" label="Cell type name"> - <validator type="empty_field"/> - </param> - <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name"> - <validator type="empty_field"/> - </param> - <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file"> - <validator type="empty_field"/> - <validator type="unspecified_build"/> - </param> - </repeat> - </when> - </conditional> + <param name="epigenetic_factor_name" type="text" value="" label="Epigenetic factor name"> + <validator type="empty_field"/> + </param> + <param name="input" type="data" format="bigwig,bam" label="BAM or BigWig file"> + <validator type="empty_field"/> + <validator type="unspecified_build"/> + </param> + </repeat> <conditional name="specify_genomic_window_cond"> <param name="specify_genomic_window" type="select" label="Select Bed file that defines genomic windows on which to process the data"> <option value="no" selected="true">No</option>