Mercurial > repos > iuc > samtools_cram_to_bam
changeset 4:1551b0dd2d16 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:11:03 +0000 |
| parents | 858ada516d8f |
| children | 634df184b2a8 |
| files | macros.xml samtools_cram_to_bam.xml test-data/sam_to_bam_out2.bam test-data/test.bam test-data/test.bed test-data/test.cram test-data/test.fa test-data/test.sam test-data/test2.cram |
| diffstat | 9 files changed, 119 insertions(+), 73 deletions(-) [+] |
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--- a/macros.xml Sat Jul 31 07:26:19 2021 +0000 +++ b/macros.xml Tue Sep 28 16:11:03 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 is mapped to the reverse strand of the reference</option> - <option value="32">Mate is mapped to the reverse strand of the reference</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 of the 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">Alignment is supplementary</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 $cond_region.select_region == 'tab':
--- a/samtools_cram_to_bam.xml Sat Jul 31 07:26:19 2021 +0000 +++ b/samtools_cram_to_bam.xml Tue Sep 28 16:11:03 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1"> +<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>convert CRAM alignments to BAM format</description> <macros> @@ -9,52 +9,31 @@ <expand macro="version_command"/> <command><![CDATA[ - #set input_cram = "input.cram" - ln -s '${input_alignment}' '${input_cram}' && - #if str( $input_alignment.metadata.cram_index ) != "None": - ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' && + @ADDTHREADS@ + ln -s '$input' input.cram && + #if str( $input.metadata.cram_index ) != "None": + ln -f -s '${input.metadata.cram_index}' input.cram.crai && #end if - #if $reference_source.reference_source_selector == 'history': - #set ref_fa = 'ref.fa' - ln -s '${reference_source.input_reference}' ref.fa && - #else: - #set ref_fa = str( $reference_source.input_reference.fields.path ) - #end if + @PREPARE_FASTA_IDX@ samtools view #if $parameter_regions.target_region == "regions_bed_file" - -L '${parameter_regions.regions_bed_file}' + -L '$parameter_regions.regions_bed_file' #end if - -@ \${GALAXY_SLOTS:-2} + -@ \$addthreads -b - -T '$ref_fa' + -T '$reffa' -o '$output_alignment' - '$input_cram' + input.cram #if $parameter_regions.target_region == "region" - '${parameter_regions.region_string}' + '$parameter_regions.region_string' #end if ]]></command> <inputs> - <param name="input_alignment" type="data" format="cram" label="CRAM alignment file"/> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> - <option value="cached">Local cache</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="input_reference" type="select" label="Reference genome"> - <options from_data_table="fasta_indexes"> - <filter type="data_meta" ref="input_alignment" key="dbkey" column="dbkey" /> - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> - </when> - <when value="history"> - <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/> - </when> - </conditional> + <param name="input" type="data" format="cram" label="CRAM alignment file"/> + <expand macro="mandatory_reference" argument="-t"/> <conditional name="parameter_regions"> <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)"> <option value="entire_input_file">Entire BAM alignment file</option> @@ -77,36 +56,33 @@ <tests> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="region" /> <param name="region_string" value="CHROMOSOME_I" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test.cram" ftype="cram" /> - <param name="reference_source_selector" value="history" /> - <param name="input_reference" value="test.fa" /> + <param name="input" value="test.cram" ftype="cram" /> + <param name="addref_select" value="history" /> + <param name="ref" value="test.fa" /> <param name="target_region" value="regions_bed_file" /> <param name="regions_bed_file" value="test.bed" ftype="bed" /> - - <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="test.bam" ftype="bam" lines_diff="4" /> </test> <test> - <param name="input_alignment" value="test2.cram" dbkey="equCab2" ftype="cram" /> - <param name="reference_source_selector" value="cached" /> - <param name="input_reference" value="equCab2chrM" /> + <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" /> + <param name="addref_select" value="cached" /> + <param name="ref" value="equCab2chrM" /> <param name="target_region" value="entire_input_file" /> - <output name="output_alignment" file="sam_to_bam_out2.bam" compare="sim_size" delta="250" /> + <output name="output_alignment" file="sam_to_bam_out2.bam" ftype="bam" lines_diff="4" /> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.bed Tue Sep 28 16:11:03 2021 +0000 @@ -0,0 +1,1 @@ +CHROMOSOME_I 1 120
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fa Tue Sep 28 16:11:03 2021 +0000 @@ -0,0 +1,3 @@ +>CHROMOSOME_I +gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc +ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcct
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Tue Sep 28 16:11:03 2021 +0000 @@ -0,0 +1,15 @@ +@HD VN:1.4 SO:unsorted +@SQ SN:CHROMOSOME_I LN:100 +@RG ID:UNKNOWN SM:UNKNOWN +@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 +@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 +SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU +SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU +SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA <?@<@A8>0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.4251890 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###########@BB=BCBBC?B>B;>B@@ADBBB@DBBBBDCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDB<DABADCACDCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.6023338 0 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAGCTAC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCDDDBCCABB=DABBA?################ RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU +SRR065390.6815812 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############?@.@?B;B0B=;<DADB@@BDDBBDDBCBCBD@CCDCCCCCCCDCCCCCCCCACCCCCCCCCCBCCCCCCDCCCCCCCCCCCBCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.6905811 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #######################BB@>A<BC>@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU +SRR065390.8289592 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################A?@C9@@BC=AABDD@A@DC@CB=@BA?6@CCAAC@+CCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU