samtools_calmd: samtools_calmd.xml annotate

annotate samtools_calmd.xml @ 7:d97988f07983 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty

author	iuc
date	Sun, 28 Jul 2019 14:46:45 -0400
parents	3b6f46492fd8
children	d29b421f5aaf

rev	line source
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	1 <tool id="samtools_calmd" name="CalMD" version="2.0.2">
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	2 <description>recalculate MD/NM tags</description>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	3 <macros>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	4 <import>macros.xml</import>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	5 </macros>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	6 <expand macro="requirements"/>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	7 <expand macro="stdio"/>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	8 <expand macro="version_command"/>
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	9 <command><![CDATA[
7 d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	10 @ADDTHREADS@
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	11 #if str( $reference_source.reference_source_selector ) == "history":
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	12 #set ref_fa = 'ref.fa'
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	13 ln -s '${reference_source.ref_fasta}' ref.fa &&
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	14 samtools faidx ref.fa &&
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	15 #else:
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	16 #set ref_fa = str( $reference_source.ref_fasta.fields.path )
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	17 #end if
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	18
7 d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	19 samtools calmd
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	20 $baq_settings.use_baq $baq_settings.modify_quality $baq_settings.extended_baq
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	21 #if str($option_set.option_sets) == 'advanced':
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	22 $option_set.change_identical -C $option_set.adjust_mq
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	23 #end if
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	24 -b
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	25 -@ \$addthreads
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	26 '$input_bam'
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	27 '$ref_fa'
d97988f07983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty iuc parents: 6 diff changeset	28 > '$calmd_output'
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	29 ]]></command>
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	30 <inputs>
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	31 <param name="input_bam" type="data" format="bam" label="BAM file to recalculate" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	32 <conditional name="reference_source">
3 609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	33 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	34 <option value="cached">Use a built-in genome</option>
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	35 <option value="history">Use a genome from the history</option>
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	36 </param>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	37 <when value="cached">
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	38 <param name="ref_fasta" type="select" label="Using reference genome">
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	39 <options from_data_table="fasta_indexes">
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	40 <filter type="data_meta" column="1" key="dbkey" ref="input_bam" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	42 </options>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	43 </param>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	44 </when>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	45 <when value="history">
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	46 <param name="ref_fasta" type="data" format="fasta" label="Using reference file" />
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	47 </when>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	48 </conditional>
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	49 <conditional name="baq_settings">
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	50 <param name="use_baq" argument="-r" type="select"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	51 label="Do you also want BAQ (Base Alignment Quality) scores to be calculated?">
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	52 <option value="">No</option>
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	53 <option value="-r">Yes, run BAQ calculation</option>
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	54 </param>
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	55 <when value="">
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	56 <param name="modify_quality" type="hidden" value="" />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	57 <param name="extended_baq" type="hidden" value="" />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	58 </when>
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	59 <when value="-r">
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	60 <param name="modify_quality" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	61 label="Use BAQ to cap read base qualities"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	62 help="By default, BAQ scores are stored in a separate BQ tag, and the read base quality string is left untouched. When you enable this option, the BAQ scores will be used directly to modify the quality string instead." />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	63 <param name="extended_baq" argument="-E" type="boolean" truevalue="-E" falsevalue="" checked="false" label="Extended BAQ for better sensitivity" />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	64 </when>
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	65 </conditional>
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	66 <conditional name="option_set">
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	67 <param name="option_sets" type="select" label="Additional options">
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	68 <option value="default">Use defaults</option>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	69 <option value="advanced">Advanced options</option>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	70 </param>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	71 <when value="default" />
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	72 <when value="advanced">
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	73 <param name="change_identical" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	74 label="Change identical bases to '='"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	75 help="Replace bases in read sequences that match the reference base at that position with an equal sign" />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	76 <param name="adjust_mq" argument="-C" type="integer" min="0" max="255" value="0"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	77 label="Coefficient to cap mapping quality of poorly mapped reads"
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	78 help="Higher values for this setting mean a stronger downgrade of the mapping quality of reads with excessive mismatches (50: recommended setting for reads aligned with BWA, 0: do not downgrade mapping qualities)" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	79 </when>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	80 </conditional>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	81 </inputs>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	82 <outputs>
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	83 <data name="calmd_output" format="bam" label="${tool.name} on ${on_string}" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	84 </outputs>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	85 <tests>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	86 <test>
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	87 <param name="use_baq" value="" />
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	88 <param name="option_sets" value="default" />
3 609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	89 <param name="input_bam" value="phiX.bam"/>
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	90 <param name="reference_source_selector" value="history" />
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	91 <param name="ref_fasta" value="phiX.fasta" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	92 <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" />
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	93 </test>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	94 <test>
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	95 <param name="use_baq" value="-r" />
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	96 <param name="extended_baq" value="true" />
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	97 <param name="option_sets" value="advanced" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	98 <param name="change_identical" value="true" />
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	99 <param name="adjust_mq" value="50" />
3 609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	100 <param name="input_bam" value="phiX.bam"/>
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	101 <param name="reference_source_selector" value="history" />
609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	102 <param name="ref_fasta" value="phiX.fasta" />
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	103 <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" />
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	104 </test>
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	105 </tests>
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	106 <help><![CDATA[
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	107 What it does
39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	108
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	109 Generates the MD tag using the ``samtools calmd`` command. If the MD tag (see
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	110 SAM format reference below for explanation of SAM/BAM tags) is already present,
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	111 this command will give a warning if the MD tag generated is different from the
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	112 existing tag.
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	113
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	114 Optionally, also generates the BQ tag to encode base alignment qualities,
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	115 caps the mapping quality of poorly mapping reads, and modifies read sequences
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	116 replacing bases matching the reference with ``=``.
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	117
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	118 Outputs a BAM file.
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	119
3 609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	120 -----
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	121
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	122 SAM/BAM tags written by this tool
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	123
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	124 From the SAM format tag specification::
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	125
3 609810451a80 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734 devteam parents: 2 diff changeset	126 MD (string) String for mismatching positions. Regex : [0-9]+(([A-Z]\|\^[A-Z]+)[0-9]+)*7
6 3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	127 NM (integer) Edit distance to the reference, including ambiguous bases but excluding clipping
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	128 BQ (string) String of offsets to base alignment quality (BAQ), of the same length as the read sequence.
3b6f46492fd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 766da8a5f0449de99c2854aacaefb80d11ad083c iuc parents: 5 diff changeset	129 At the i-th read base, BAQ i = Q i − (BQ i − 64) where Q i is the i-th base quality.
0 39472bc02d8d Uploaded initial tool tarball. devteam parents: diff changeset	130
5 ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	131 See references for more information about SAM format tags.
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	132 ]]></help>
ed0f72810fd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_calmd commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 iuc parents: 3 diff changeset	133 <expand macro="citations"/>
1 c61c0d198e4a Uploaded devteam parents: 0 diff changeset	134 </tool>

Mercurial > repos > devteam > samtools_calmd

annotate samtools_calmd.xml @ 7:d97988f07983 draft