samtools_slice_bam: samtools_slice

annotate samtools_slice_bam.xml @ 6:b8beef827165 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

author	iuc
date	Sun, 08 Sep 2024 03:26:35 +0000
parents	b5c88b7b153e
children

rev	line source
5 b5c88b7b153e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit cd62639660bef041ba14ecff337fb98e84e75d8a iuc parents: 4 diff changeset	1 <tool id="samtools_slice_bam" name="Slice" version="2.0.3" profile="@PROFILE@">
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	2 <description>BAM by genomic regions</description>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	3 <macros>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	4 <import>macros.xml</import>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	5 </macros>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	6
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	7 <expand macro="requirements"/>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	8 <expand macro="stdio"/>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	9 <expand macro="version_command"/>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	10
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	11 <command><![CDATA[
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	12 ln -s '${input_bam}' temp_input.bam &&
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	13 ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	14
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	15 #if str($slice_method.slice_method_selector) == "bed":
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	16 samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	17 #elif str($slice_method.slice_method_selector) == "chr":
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	18 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	19 ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	20 #elif str($slice_method.slice_method_selector) == "man":
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	21 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	22
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	23 #for $region in $slice_method.regions:
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	24 "${region.chrom}:${region.start}-${region.end}"
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	25 #end for
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	26 &&
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	27 #end if
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	28
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	29 samtools sort
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	30 -O bam
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	31 -T "\${TMPDIR:-.}"
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	32 -@ \${GALAXY_SLOTS:-1}
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	33 -o '${output_bam}'
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	34 unsorted_output.bam
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	35 ]]></command>
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	36 <inputs>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	37 <param name="input_bam" type="data" format="bam" label="Select BAM dataset to slice" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	38 <conditional name="slice_method">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	39 <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	40 <option value="bed">using a list of intervals from a BED dataset</option>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	41 <option value="chr">by chromosomes/contigs present in the BAM dataset</option>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	42 <option value="man">by chromosomes/contigs and coordinates</option>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	43 </param>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	44 <when value="bed">
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	45 <param name="input_interval" type="data" format="bed" label="BED file" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	46 </when>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	47 <when value="chr">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	48 <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	49
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	50 <!-- The options tagset below extracts reference names from bam file metadata -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	51 <!-- This will not work with bed files with old style metadata. However this -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	52 <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	53 <!-- The pencil icon and settind datatype to "bam" -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	54 <!-- This change has been commited in the following pull request: -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	55 <!-- https://github.com/galaxyproject/galaxy/pull/107 -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	56
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	57 <options>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	58 <filter type="data_meta" ref="input_bam" key="reference_names" />
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	59 </options>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	60 </param>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	61 </when>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	62 <when value="man">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	63 <repeat name="regions" title="Regions" min="1">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	64 <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	65
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	66 <!-- See comments above -->
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	67
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	68 <options>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	69 <filter type="data_meta" ref="input_bam" key="reference_names" />
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	70 </options>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	71 </param>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	72 <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	73 <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	74 </repeat>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	75 </when>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	76 </conditional>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	77 </inputs>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	78 <outputs>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	79 <data name="output_bam" format="bam" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	80 </outputs>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	81 <tests>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	82 <test>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	83 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	84 <param name="slice_method_selector" value="bed"/>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	85 <param name="input_interval" ftype="bed" value="bam-slice.bed" />
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	86 <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" lines_diff="4" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	87 </test>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	88 <test>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	89 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	90 <param name="slice_method_selector" value="chr"/>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	91 <param name="refs" value="chrM" />
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	92 <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" lines_diff="4" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	93 </test>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	94 <test>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	95 <param name="input_bam" ftype="bam" value="bam-slice-input.bam" />
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	96 <param name="slice_method_selector" value="man"/>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	97 <param name="chrom" value="chrM" />
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	98 <param name="start" value="1" />
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	99 <param name="end" value="1000" />
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	100 <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" lines_diff="4"/>
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	101 </test>
2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	102 </tests>
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	103 <help><![CDATA[
0 68ba55e96489 Uploaded tool tarball. devteam parents: diff changeset	104 What it does
68ba55e96489 Uploaded tool tarball. devteam parents: diff changeset	105
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	106 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.
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	107 BED datasets can be obtained from Get Data -> UCSC Main.
0 68ba55e96489 Uploaded tool tarball. devteam parents: diff changeset	108
4 344fc91e1bfd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" iuc parents: 3 diff changeset	109 This tool is based on ``samtools view`` command.
0 68ba55e96489 Uploaded tool tarball. devteam parents: diff changeset	110
2 2b474ebbfc7d Uploaded devteam parents: 1 diff changeset	111 @no-chrom-options@
3 a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	112 ]]></help>
a4a10c7924d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 2 diff changeset	113 <expand macro="citations"/>
0 68ba55e96489 Uploaded tool tarball. devteam parents: diff changeset	114 </tool>

Mercurial > repos > devteam > samtools_slice_bam

annotate samtools_slice_bam.xml @ 6:b8beef827165 draft default tip