| Previous changeset 4:2f41fac75575 (2016-12-07) Next changeset 6:e9db5497e675 (2016-12-07) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7 |
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modified:
lumpy.xml |
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| diff -r 2f41fac75575 -r 745cbe841e40 lumpy.xml --- a/lumpy.xml Wed Dec 07 09:52:03 2016 -0500 +++ b/lumpy.xml Wed Dec 07 12:26:42 2016 -0500 |
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| @@ -3,18 +3,18 @@ <requirements> <requirement type="package" version="0.2.12">lumpy-sv</requirement> <requirement type="package" version="1.3.1">samtools</requirement> - <requirement type="package" version="1.11.2">numpy</requirement> + <requirement type="package" version="1.11.2=py27">numpy</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <version_command>lumpy --version</version_command> - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ #if $analysis_type.analysis_type_list == "one_sample": - ln -f -s $analysis_type.input_file input.bam && + ln -f -s '$analysis_type.input_file' input.bam && #else: - ln -f -s $analysis_type.input_file input.A.bam && - ln -f -s $analysis_type.input_fileB input.B.bam && + ln -f -s '$analysis_type.input_file' input.A.bam && + ln -f -s '$analysis_type.input_fileB' input.B.bam && #end if #if $analysis_type.analysis_type_list == "one_sample": @@ -146,21 +146,21 @@ </inputs> <outputs> - <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> + <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> + <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> - <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> - <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> + <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)"/> + <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)"> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> - <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> + <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> + <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> @@ -217,6 +217,7 @@ Summary: Find structural variations in various signals. Options:: +<![CDATA[ -g Genome file (defines chromosome order) -e Show evidence for each call @@ -228,31 +229,31 @@ -t temp file prefix, must be to a writeable directory -P output probability curve for each variant -b output BEDPE instead of VCF - -sr bam_file:<file name>, - id:<sample name>, - back_distance:<distance>, - min_mapping_threshold:<mapping quality>, - weight:<sample weight>, - min_clip:<minimum clip length>, - read_group:<string> + -sr bam_file:<file name>, + id:<sample name>, + back_distance:<distance>, + min_mapping_threshold:<mapping quality>, + weight:<sample weight>, + min_clip:<minimum clip length>, + read_group:<string> - -pe bam_file:<file name>, - id:<sample name>, - histo_file:<file name>, - mean:<value>, - stdev:<value>, - read_length:<length>, - min_non_overlap:<length>, - discordant_z:<z value>, - back_distance:<distance>, - min_mapping_threshold:<mapping quality>, - weight:<sample weight>, - read_group:<string> + -pe bam_file:<file name>, + id:<sample name>, + histo_file:<file name>, + mean:<value>, + stdev:<value>, + read_length:<length>, + min_non_overlap:<length>, + discordant_z:<z value>, + back_distance:<distance>, + min_mapping_threshold:<mapping quality>, + weight:<sample weight>, + read_group:<string> - -bedpe bedpe_file:<bedpe file>, - id:<sample name>, - weight:<sample weight> - + -bedpe bedpe_file:<bedpe file>, + id:<sample name>, + weight:<sample weight> +]]> </help> <citations> |