Mercurial > repos > devteam > picard
changeset 31:585027e65f3b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84
| author | iuc |
|---|---|
| date | Sat, 25 Feb 2023 20:33:49 +0000 |
| parents | b502c227b5e6 |
| children | f9242e01365a |
| files | picard_CollectAlignmentSummaryMetrics.xml picard_CollectBaseDistributionByCycle.xml picard_CollectInsertSizeMetrics.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_MergeBamAlignment.xml picard_SamToFastq.xml |
| diffstat | 7 files changed, 27 insertions(+), 41 deletions(-) [+] |
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--- a/picard_CollectAlignmentSummaryMetrics.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>writes a file containing summary alignment metrics</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -71,13 +71,15 @@ </inputs> <outputs> - <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tablular"/> </outputs> <tests> <test> <param name="bisulphite" value="false" /> - <param name="sorted" value="true" /> - <param name="adaptors" value="" /> + <param name="assume_sorted" value="true" /> + <repeat name="adapters"> + <param name="adapter" value = ""/> + </repeat> <param name="maxinsert" value="100000" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="picard_CASM_ref.fa" />
--- a/picard_CollectBaseDistributionByCycle.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_CollectBaseDistributionByCycle.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -59,8 +59,8 @@ </inputs> <outputs> - <data format="tabular" name="outFile"/> - <data format="pdf" name="pdfFile"/> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tabular"/> + <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: PDF"/> </outputs> <tests>
--- a/picard_CollectInsertSizeMetrics.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_CollectInsertSizeMetrics.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>plots distribution of insert sizes</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> @@ -72,8 +72,8 @@ </inputs> <outputs> - <data format="tabular" name="outFile"/> - <data format="pdf" name="histFile"/> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tabular"/> + <data format="pdf" name="histFile" label="${tool.name} on ${on_string}: PDF"/> </outputs> <tests>
--- a/picard_MarkDuplicates.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_MarkDuplicates.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">3</token> + <token name="@WRAPPER_VERSION@">4</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -56,7 +56,7 @@ <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default='' (uses : separation)"> <expand macro="sanitize_query" /> </param> - <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> + <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices. Typically 'RX' "/> @@ -65,8 +65,8 @@ </inputs> <outputs> - <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> - <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> + <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/> </outputs> <tests>
--- a/picard_MarkDuplicatesWithMateCigar.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_MarkDuplicatesWithMateCigar.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>examine aligned records in BAM datasets to locate duplicate molecules</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> + <token name="@WRAPPER_VERSION@">3</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -55,15 +55,15 @@ <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> <expand macro="sanitize_query" /> </param> - <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> + <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="5000" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> <expand macro="VS" /> </inputs> <outputs> - <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> - <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> + <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: metrics"/> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/> </outputs> <tests>
--- a/picard_MergeBamAlignment.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_MergeBamAlignment.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>merge alignment data with additional info stored in an unmapped BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">2</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -176,7 +176,7 @@ <expand macro="VS" /> </inputs> <outputs> - <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/> </outputs> <tests> <test> @@ -191,7 +191,7 @@ <param name="max_insertions_or_deletions" value="1"/> <param name="read1_trim" value="0"/> <param name="read2_trim" value="0"/> - <param name="orientation" value="FR"/> + <param name="orientations" value="FR"/> <param name="aligner_proper_pair_flags" value="False"/> <param name="primary_alignment_strategy" value="BestMapq"/> <param name="clip_overlapping_reads" value="True"/>
--- a/picard_SamToFastq.xml Mon Aug 22 09:56:00 2022 +0000 +++ b/picard_SamToFastq.xml Sat Feb 25 20:33:49 2023 +0000 @@ -2,7 +2,7 @@ <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> + <token name="@WRAPPER_VERSION@">3</token> </macros> <xrefs> <xref type="bio.tools">picard_samtofastq</xref> @@ -107,7 +107,6 @@ <test> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_interleaved" /> - <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> @@ -122,7 +121,6 @@ <test> <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/> <param name="single_or_paired" value="pe_sep" /> - <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> @@ -139,7 +137,6 @@ <test> <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/> <param name="single_or_paired" value="se" /> - <param name="output_per_rg" value="false"/> <param name="re_reverse" value="true"/> <param name="include_non_pf_reads" value="false"/> <param name="clipping_attribute" value="" /> @@ -164,34 +161,21 @@ .. class:: warningmark -**DANGER: Multiple Outputs** - -Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing! - @dataset_collections@ @description@ FASTQ=File F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). - Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) + Required. SECOND_END_FASTQ=File F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null. - Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) + UNPAIRED_FASTQ=File FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default - value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG) - - OUTPUT_PER_RG=Boolean - OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is - paired). Default value: false. Possible values: {true, false} Cannot be used in - conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) - - OUTPUT_DIR=File - ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. - Default value: null. + value: null. RE_REVERSE=Boolean RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them