Mercurial > repos > devteam > samtools_flagstat
changeset 10:9b44224f5a76 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:02:06 +0000 |
| parents | 5fbe9dcaef98 |
| children | |
| files | macros.xml samtools_flagstat.xml test-data/samtools_flagstat_out1.json test-data/samtools_flagstat_out1.tsv test-data/samtools_flagstat_out1.txt |
| diffstat | 5 files changed, 169 insertions(+), 24 deletions(-) [+] |
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--- a/macros.xml Fri Sep 06 11:21:12 2019 -0400 +++ b/macros.xml Tue Sep 28 16:02:06 2021 +0000 @@ -5,10 +5,16 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.9</token> - <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> + <token name="@TOOL_VERSION@">1.13</token> + <token name="@PROFILE@">20.05</token> + <token name="@FLAGS@"><![CDATA[ + #set $flags = 0 + #if $filter + #set $flags = sum(map(int, str($filter).split(','))) + #end if + ]]></token> <token name="@PREPARE_IDX@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices ln -s '$input' infile && #if $input.is_of_type('bam'): #if str( $input.metadata.bam_index ) != "None": @@ -25,7 +31,7 @@ #end if ]]></token> <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ - ##prepare input and indices + ##prepare input and indices #for $i, $bam in enumerate( $input_bams ): ln -s '$bam' '${i}' && #if $bam.is_of_type('bam'): @@ -63,6 +69,51 @@ #set reffai=None #end if ]]></token> + + <xml name="optional_reference"> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="no">No</option> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="no"/> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + </options> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> + </param> + </when> + </conditional> + </xml> + <xml name="mandatory_reference" token_help="" token_argument=""> + <conditional name="addref_cond"> + <param name="addref_select" type="select" label="Use a reference sequence"> + <help>@HELP@</help> + <option value="history">Use a genome/index from the history</option> + <option value="cached">Use a built-in genome</option> + </param> + <when value="history"> + <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> + </when> + <when value="cached"> + <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> + <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> + </options> + </param> + </when> + </conditional> + </xml> + + <token name="@ADDTHREADS@"><![CDATA[ ##compute the number of ADDITIONAL threads to be used by samtools (-@) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && @@ -70,28 +121,28 @@ <token name="@ADDMEMORY@"><![CDATA[ ##compute the number of memory available to samtools sort (-m) ##use only 75% of available: https://github.com/samtools/samtools/issues/831 - addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && + addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && ]]></token> <xml name="seed_input"> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> </xml> - <xml name="flag_options"> - <option value="1">read is paired</option> - <option value="2">read is mapped in a proper pair</option> - <option value="4">read is unmapped</option> - <option value="8">mate is unmapped</option> - <option value="16">read reverse strand</option> - <option value="32">mate reverse strand</option> - <option value="64">read is the first in a pair</option> - <option value="128">read is the second in a pair</option> - <option value="256">alignment or read is not primary</option> - <option value="512">read fails platform/vendor quality checks</option> - <option value="1024">read is a PCR or optical duplicate</option> - <option value="2048">supplementary alignment</option> + <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false"> + <option value="1" selected="@S1@">Read is paired</option> + <option value="2" selected="@S2@">Read is mapped in a proper pair</option> + <option value="4" selected="@S4@">Read is unmapped</option> + <option value="8" selected="@S8@">Mate is unmapped</option> + <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> + <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> + <option value="64" selected="@S64@">Read is the first in a pair</option> + <option value="128" selected="@S128@">Read is the second in a pair</option> + <option value="256" selected="@S256@">Alignment of the read is not primary</option> + <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> + <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> + <option value="2048" selected="@S2048@">Alignment is supplementary</option> </xml> - <!-- region specification macros and tokens for tools that allow the specification + <!-- region specification macros and tokens for tools that allow the specification of region by bed file / space separated list of regions --> <token name="@REGIONS_FILE@"><![CDATA[ #if $cond_region.select_region == 'tab':
--- a/samtools_flagstat.xml Fri Sep 06 11:21:12 2019 -0400 +++ b/samtools_flagstat.xml Tue Sep 28 16:02:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.3"> +<tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.4" profile="@PROFILE@"> <description>tabulate descriptive stats for BAM datset</description> <macros> @@ -10,21 +10,46 @@ <command><![CDATA[ @ADDTHREADS@ - samtools flagstat -@ \$addthreads '$input1' > '$output1' + samtools flagstat -@ \$addthreads + #if $output_fmt != 'txt' + --output-fmt $output_fmt + #end if + '$input1' + > '$output1' ]]></command> <inputs> <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" /> + <param argument="--output-fmt" type="select" label="Output format"> + <option value="txt">txt</option> + <option value="tsv">tsv</option> + <option value="json">json</option> + </param> </inputs> <outputs> - <data name="output1" format="txt" /> + <data name="output1" format="txt"> + <change_format> + <when input="output_fmt" value="tsv" format="tabular" /> + <when input="output_fmt" value="json" format="json" /> + </change_format> + </data> </outputs> <tests> <test> <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> - <output name="output1" file="samtools_flagstat_out1.txt" /> + <output name="output1" file="samtools_flagstat_out1.txt" ftype="txt"/> + </test> + <test> + <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> + <param name="output_fmt" value="tsv"/> + <output name="output1" file="samtools_flagstat_out1.tsv" ftype="tabular" /> + </test> + <test> + <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" /> + <param name="output_fmt" value="json"/> + <output name="output1" file="samtools_flagstat_out1.json" ftype="json" /> </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_flagstat_out1.json Tue Sep 28 16:02:06 2021 +0000 @@ -0,0 +1,46 @@ +{ + "QC-passed reads": { + "total": 200, + "primary": 200, + "secondary": 0, + "supplementary": 0, + "duplicates": 0, + "primary duplicates": 0, + "mapped": 25, + "mapped %": 12.50, + "primary mapped": 25, + "primary mapped %": 12.50, + "paired in sequencing": 200, + "read1": 100, + "read2": 100, + "properly paired": 0, + "properly paired %": 0.00, + "with itself and mate mapped": 0, + "singletons": 25, + "singletons %": 12.50, + "with mate mapped to a different chr": 0, + "with mate mapped to a different chr (mapQ >= 5)": 0 + }, + "QC-failed reads": { + "total": 0, + "primary": 0, + "secondary": 0, + "supplementary": 0, + "duplicates": 0, + "primary duplicates": 0, + "mapped": 0, + "mapped %": null, + "primary mapped": 0, + "primary mapped %": null, + "paired in sequencing": 0, + "read1": 0, + "read2": 0, + "properly paired": 0, + "properly paired %": null, + "with itself and mate mapped": 0, + "singletons": 0, + "singletons %": null, + "with mate mapped to a different chr": 0, + "with mate mapped to a different chr (mapQ >= 5)": 0 + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_flagstat_out1.tsv Tue Sep 28 16:02:06 2021 +0000 @@ -0,0 +1,20 @@ +200 0 total (QC-passed reads + QC-failed reads) +200 0 primary +0 0 secondary +0 0 supplementary +0 0 duplicates +0 0 primary duplicates +25 0 mapped +12.50% N/A mapped % +25 0 primary mapped +12.50% N/A primary mapped % +200 0 paired in sequencing +100 0 read1 +100 0 read2 +0 0 properly paired +0.00% N/A properly paired % +0 0 with itself and mate mapped +25 0 singletons +12.50% N/A singletons % +0 0 with mate mapped to a different chr +0 0 with mate mapped to a different chr (mapQ>=5)
--- a/test-data/samtools_flagstat_out1.txt Fri Sep 06 11:21:12 2019 -0400 +++ b/test-data/samtools_flagstat_out1.txt Tue Sep 28 16:02:06 2021 +0000 @@ -1,8 +1,11 @@ 200 + 0 in total (QC-passed reads + QC-failed reads) +200 + 0 primary 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates +0 + 0 primary duplicates 25 + 0 mapped (12.50% : N/A) +25 + 0 primary mapped (12.50% : N/A) 200 + 0 paired in sequencing 100 + 0 read1 100 + 0 read2