| Previous changeset 3:a4a10c7924d1 (2017-05-09) Next changeset 5:b5c88b7b153e (2023-11-20) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" |
|
modified:
macros.xml samtools_slice_bam.xml test-data/bam-slice-test1.bam test-data/bam-slice-test2.bam test-data/bam-slice-test3.bam |
| b |
| diff -r a4a10c7924d1 -r 344fc91e1bfd macros.xml --- a/macros.xml Tue May 09 11:17:27 2017 -0400 +++ b/macros.xml Tue Sep 28 16:16:30 2021 +0000 |
| [ |
| b'@@ -1,11 +1,182 @@\n <macros>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.3.1">samtools</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>\n <yield/>\n </requirements>\n </xml>\n- <token name="@TOOL_VERSION@">1.3.1</token>\n+ <token name="@TOOL_VERSION@">1.13</token>\n+ <token name="@PROFILE@">20.05</token>\n+ <token name="@FLAGS@"><![CDATA[\n+ #set $flags = 0\n+ #if $filter\n+ #set $flags = sum(map(int, str($filter).split(\',\')))\n+ #end if\n+ ]]></token>\n+ <token name="@PREPARE_IDX@"><![CDATA[\n+ ##prepare input and indices\n+ ln -s \'$input\' infile &&\n+ #if $input.is_of_type(\'bam\'):\n+ #if str( $input.metadata.bam_index ) != "None":\n+ ln -s \'${input.metadata.bam_index}\' infile.bai &&\n+ #else:\n+ samtools index infile infile.bai &&\n+ #end if\n+ #elif $input.is_of_type(\'cram\'):\n+ #if str( $input.metadata.cram_index ) != "None":\n+ ln -s \'${input.metadata.cram_index}\' infile.crai &&\n+ #else:\n+ samtools index infile infile.crai &&\n+ #end if\n+ #end if\n+ ]]></token>\n+ <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[\n+ ##prepare input and indices\n+ #for $i, $bam in enumerate( $input_bams ):\n+ ln -s \'$bam\' \'${i}\' &&\n+ #if $bam.is_of_type(\'bam\'):\n+ #if str( $bam.metadata.bam_index ) != "None":\n+ ln -s \'${bam.metadata.bam_index}\' \'${i}.bai\' &&\n+ #else:\n+ samtools index \'${i}\' \'${i}.bai\' &&\n+ #end if\n+ #elif $bam.is_of_type(\'cram\'):\n+ #if str( $bam.metadata.cram_index ) != "None":\n+ ln -s \'${bam.metadata.cram_index}\' \'${i}.crai\' &&\n+ #else:\n+ samtools index \'${i}\' \'${i}.crai\' &&\n+ #end if\n+ #end if\n+ #end for\n+ ]]></token>\n+ <token name="@PREPARE_FASTA_IDX@"><![CDATA[\n+ ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")\n+ ##and sets the -t/-T parameters accordingly:\n+ ##- in case of history a symbolic link is used because samtools (view) will generate\n+ ## the index which might not be possible in the directory containing the fasta file\n+ ##- in case of cached the absolute path is used which allows to read the cram file\n+ ## without specifying the reference\n+ #if $addref_cond.addref_select == "history":\n+ ln -s \'${addref_cond.ref}\' reference.fa &&\n+ samtools faidx reference.fa &&\n+ #set reffa="reference.fa"\n+ #set reffai="reference.fa.fai"\n+ #elif $addref_cond.addref_select == "cached":\n+ #set reffa=str($addref_cond.ref.fields.path)\n+ #set reffai=str($addref_cond.ref.fields.path)+".fai"\n+ #else\n+ #set reffa=None\n+ #set reffai=None\n+ #end if\n+ ]]></token>\n+\n+ <xml name="optional_reference">\n+ <conditional name="addref_cond">\n+ <param name="addref_select" type="select" label="Use a reference sequence">\n+ <help>@HELP@</help>\n+ <option value="no">No</option>\n+ <option value="history">Use a genome/index from the history</option>\n+ <option value="cached">Use a built-in genome</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="history">\n+ <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>\n+ </when>\n+ <when value="cached">\n+ <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">\n+ <options from_data_table="fasta_indexes">\n+ '..b' paired</option>\n+ <option value="2" selected="@S2@">Read is mapped in a proper pair</option>\n+ <option value="4" selected="@S4@">Read is unmapped</option>\n+ <option value="8" selected="@S8@">Mate is unmapped</option>\n+ <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>\n+ <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>\n+ <option value="64" selected="@S64@">Read is the first in a pair</option>\n+ <option value="128" selected="@S128@">Read is the second in a pair</option>\n+ <option value="256" selected="@S256@">Alignment of the read is not primary</option>\n+ <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>\n+ <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>\n+ <option value="2048" selected="@S2048@">Alignment is supplementary</option>\n+ </xml>\n+\n+ <!-- region specification macros and tokens for tools that allow the specification\n+ of region by bed file / space separated list of regions -->\n+ <token name="@REGIONS_FILE@"><![CDATA[\n+ #if $cond_region.select_region == \'tab\':\n+ -t \'$cond_region.targetregions\'\n+ #end if\n+ ]]></token>\n+ <token name="@REGIONS_MANUAL@"><![CDATA[\n+ #if $cond_region.select_region == \'text\':\n+ #for $i, $x in enumerate($cond_region.regions_repeat):\n+ \'${x.region}\'\n+ #end for\n+ #end if\n+ ]]></token>\n+ <xml name="regions_macro">\n+ <conditional name="cond_region">\n+ <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">\n+ <option value="no" selected="True">No</option>\n+ <option value="text">Manualy specify regions</option>\n+ <option value="tab">Regions from tabular file</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="text">\n+ <repeat name="regions_repeat" min="1" default="1" title="Regions">\n+ <param name="region" type="text" label="region" help="format chr:from-to">\n+ <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\\s\'\\":]+(:\\d+(-\\d+){0,1}){0,1}$</validator>\n+ </param>\n+ </repeat>\n+ </when>\n+ <when value="tab">\n+ <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />\n+ </when>\n+ </conditional>\n+ </xml>\n+\n <xml name="citations">\n <citations>\n <citation type="bibtex">\n@@ -49,21 +220,4 @@\n <exit_code range="1:" level="fatal" description="Error" />\n </stdio>\n </xml>\n- <token name="@no-chrom-options@">\n------\n-\n-.. class:: warningmark\n-\n-**No options available? How to re-detect metadata**\n-\n-If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:\n-\n-1. Click on the **pencil** icon adjacent to the dataset in the history\n-2. A new menu will appear in the center pane of the interface\n-3. Click **Datatype** tab\n-4. Set **New Type** to **BAM**\n-5. Click **Save**\n-\n-The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.\n- </token>\n </macros>\n' |
| b |
| diff -r a4a10c7924d1 -r 344fc91e1bfd samtools_slice_bam.xml --- a/samtools_slice_bam.xml Tue May 09 11:17:27 2017 -0400 +++ b/samtools_slice_bam.xml Tue Sep 28 16:16:30 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="samtools_slice_bam" name="Slice" version="2.0.1"> +<tool id="samtools_slice_bam" name="Slice" version="2.0.2" profile="@PROFILE@"> <description>BAM by genomic regions</description> <macros> <import>macros.xml</import> @@ -13,12 +13,12 @@ ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai && #if str($slice_method.slice_method_selector) == "bed": - samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && + samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && #elif str($slice_method.slice_method_selector) == "chr": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } && #elif str($slice_method.slice_method_selector) == "man": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam + samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam #for $region in $slice_method.regions: "${region.chrom}:${region.start}-${region.end}" @@ -28,7 +28,7 @@ samtools sort -O bam - -T sorted + -T "\${TMPDIR:-.}" -@ \${GALAXY_SLOTS:-1} -o '${output_bam}' unsorted_output.bam @@ -83,13 +83,13 @@ <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="bed"/> <param name="input_interval" ftype="bed" value="bam-slice.bed" /> - <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" /> </test> <test> <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="chr"/> <param name="refs" value="chrM" /> - <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" /> </test> <test> <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> @@ -97,7 +97,7 @@ <param name="chrom" value="chrM" /> <param name="start" value="1" /> <param name="end" value="1000" /> - <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" /> + <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help><![CDATA[ @@ -106,7 +106,7 @@ Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**. -This tool is based on ``samtools view`` command. +This tool is based on ``samtools view`` command. @no-chrom-options@ ]]></help> |
| b |
| diff -r a4a10c7924d1 -r 344fc91e1bfd test-data/bam-slice-test1.bam |
| b |
| Binary file test-data/bam-slice-test1.bam has changed |
| b |
| diff -r a4a10c7924d1 -r 344fc91e1bfd test-data/bam-slice-test2.bam |
| b |
| Binary file test-data/bam-slice-test2.bam has changed |
| b |
| diff -r a4a10c7924d1 -r 344fc91e1bfd test-data/bam-slice-test3.bam |
| b |
| Binary file test-data/bam-slice-test3.bam has changed |