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synced 2026-10-24 02:04:04 +08:00
fixing on_string again. Add job title to tophat2
This commit is contained in:
Ross Lazarus
@@ -106,6 +106,7 @@ class Configuration( object ):
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self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
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self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
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self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) )
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self.use_data_id_on_string = string_as_bool( kwargs.get( "use_data_id_on_string", "False" ) )
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self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) )
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self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) )
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self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ]
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@@ -191,14 +191,20 @@ class DefaultToolAction( object ):
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data = data.to_history_dataset_association( None )
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inp_data[name] = data
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else: # HDA
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if data.hid:
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input_names.append( 'data %s' % data.hid )
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# else: # HDA
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# if data.hid:
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# input_names.append( 'data %s' % data.hid )
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input_ext = data.ext
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if data.dbkey not in [None, '?']:
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input_dbkey = data.dbkey
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data_name_sane = re.sub('[^a-zA-Z0-9_]+', '', data.name)
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if trans.app.config.use_data_id_on_string:
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# we want names in our on_strings not numbers
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input_names.append(data_name_sane)
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else:
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if data.hid:
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input_names.append('data %s' % data.hid)
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# Collect chromInfo dataset and add as parameters to incoming
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db_datasets = {}
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db_dataset = trans.db_dataset_for( input_dbkey )
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@@ -232,11 +238,14 @@ class DefaultToolAction( object ):
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if len( input_names ) == 1:
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on_text = input_names[0]
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elif len( input_names ) == 2:
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on_text = '%s and %s' % tuple(input_names[0:2])
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#on_text = '%s and %s' % tuple(input_names[0:2])
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on_text = '%s_%s' % tuple(input_names[0:2])
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elif len( input_names ) == 3:
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on_text = '%s, %s, and %s' % tuple(input_names[0:3])
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#on_text = '%s, %s, and %s' % tuple(input_names[0:3])
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on_text = '%s_%s_%s' % tuple(input_names[0:3])
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elif len( input_names ) > 3:
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on_text = '%s, %s, and others' % tuple(input_names[0:2])
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#on_text = '%s, %s, and others' % tuple(input_names[0:2])
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on_text = '%s_%s_and_others' % tuple(input_names[0:2])
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else:
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on_text = ""
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# Add the dbkey to the incoming parameters
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@@ -126,6 +126,14 @@
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</command>
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<inputs>
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<param name="jobname" type="text" value="Tophat2" size="80" label="Job title for outputs"
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help="Output name to remind you what this was for">
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<sanitizer invalid_char="">
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<valid initial="string.letters,string.digits">
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<add value="_" />
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</valid>
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</sanitizer>
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</param>
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<conditional name="singlePaired">
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<param name="sPaired" type="select" label="Is this library mate-paired?">
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<option value="single">Single-end</option>
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@@ -273,19 +281,19 @@
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</stdio>
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<outputs>
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<data format="tabular" name="fusions" label="${on_string}_tophat2fus.xls" from_work_dir="tophat_out/fusions.out">
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<data format="tabular" name="fusions" label="${on_string}_${jobname}_fusions.xls" from_work_dir="tophat_out/fusions.out">
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<filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
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</data>
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<data format="bed" name="insertions" label="${on_string}_tophat2ins.bed" from_work_dir="tophat_out/insertions.bed">
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<data format="bed" name="insertions" label="${on_string}_${jobname}_ins.bed" from_work_dir="tophat_out/insertions.bed">
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<expand macro="dbKeyActions" />
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</data>
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<data format="bed" name="deletions" label="${on_string}_tophhat2del.bed" from_work_dir="tophat_out/deletions.bed">
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<data format="bed" name="deletions" label="${on_string}_${jobname}_del.bed" from_work_dir="tophat_out/deletions.bed">
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<expand macro="dbKeyActions" />
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</data>
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<data format="bed" name="junctions" label="${on_string}tophat2sj.bed" from_work_dir="tophat_out/junctions.bed">
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<data format="bed" name="junctions" label="${on_string}_${jobname}_splicejunc.bed" from_work_dir="tophat_out/junctions.bed">
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<expand macro="dbKeyActions" />
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</data>
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<data format="bam" name="accepted_hits" label="${on_string}tophat2hits.bam" from_work_dir="tophat_out/accepted_hits.bam">
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<data format="bam" name="accepted_hits" label="${on_string}_${jobname}_hits.bam" from_work_dir="tophat_out/accepted_hits.bam">
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<expand macro="dbKeyActions" />
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</data>
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</outputs>
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@@ -95,15 +95,14 @@
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#end if
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## view/sort and output file
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| samtools view -Su - | samtools sort -o - - > $output;
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| samtools view -Su - | samtools sort -o - - > $output
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## rename unaligned sequence files
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#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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#set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' )
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#set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' )
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mv $left $output_unaligned_reads_l;
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mv $right $output_unaligned_reads_r;
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;mv $left $output_unaligned_reads_l;
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mv $right $output_unaligned_reads_r
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#end if
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</command>
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@@ -218,7 +217,7 @@
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<!-- define outputs -->
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<outputs>
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<data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_{jobtitle}_unaligL.fastq" >
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<data format="fastqsanger" name="output_unaligned_reads_l" label="${on_string}_${jobtitle}_unaligL.fastq" >
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<filter>unaligned_file is True</filter>
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<actions>
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<action type="format">
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@@ -226,7 +225,7 @@
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</action>
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</actions>
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</data>
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<data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_{jobtitle}_unaligR.fastq)">
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<data format="fastqsanger" name="output_unaligned_reads_r" label="${on_string}_${jobtitle}_unaligR.fastq)">
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<filter>library['type'] == "paired" and unaligned_file is True</filter>
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<actions>
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<action type="format">
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@@ -234,7 +233,7 @@
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</action>
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</actions>
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</data>
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<data format="bam" name="output" label="${tool.name} on ${on_string}_{jobtitle}_aligned.bam">
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<data format="bam" name="output" label="${tool.name} on ${on_string}_${jobtitle}_aligned.bam">
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<actions>
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<conditional name="reference_genome.source">
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<when value="indexed">
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