| Previous changeset 6:88eedb4abea0 (2018-10-14) Next changeset 8:a53efedba9e7 (2023-11-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b" |
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modified:
bam_to_sam.xml macros.xml test-data/bam_to_sam_out1.sam test-data/bam_to_sam_out2.sam |
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| diff -r 88eedb4abea0 -r 10184eaa85fc bam_to_sam.xml --- a/bam_to_sam.xml Sun Oct 14 12:01:48 2018 -0400 +++ b/bam_to_sam.xml Tue Sep 28 16:10:41 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.2" profile="@PROFILE@"> <description>convert BAM to SAM</description> <macros> @@ -28,12 +28,12 @@ <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="-h" /> - <output file="bam_to_sam_out1.sam" name="output1" /> + <output file="bam_to_sam_out1.sam" name="output1" lines_diff="2" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> <param name="header" value="-H" /> - <output file="bam_to_sam_out2.sam" name="output1" /> + <output file="bam_to_sam_out2.sam" name="output1" lines_diff="2" /> </test> <test> <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" /> |
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| diff -r 88eedb4abea0 -r 10184eaa85fc macros.xml --- a/macros.xml Sun Oct 14 12:01:48 2018 -0400 +++ b/macros.xml Tue Sep 28 16:10:41 2021 +0000 |
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| @@ -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': |
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| diff -r 88eedb4abea0 -r 10184eaa85fc test-data/bam_to_sam_out1.sam --- a/test-data/bam_to_sam_out1.sam Sun Oct 14 12:01:48 2018 -0400 +++ b/test-data/bam_to_sam_out1.sam Tue Sep 28 16:10:41 2021 +0000 |
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| @@ -4,6 +4,7 @@ @SQ SN:chr8 LN:202 @RG ID:0 SM:Hi,Mom! @PG ID:1 PN:Hey! VN:2.0 +@PG ID:samtools PN:samtools PP:1 VN:1.12 CL:samtools view -o /tmp/tmpl_eh5cxt/files/3/b/2/dataset_3b2eeebc-108d-4ce9-a5b9-17e224264121.dat -h /tmp/tmpl_eh5cxt/files/1/2/d/dataset_12de9904-ebd8-436b-a125-8f034068385e.dat both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 |
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| diff -r 88eedb4abea0 -r 10184eaa85fc test-data/bam_to_sam_out2.sam --- a/test-data/bam_to_sam_out2.sam Sun Oct 14 12:01:48 2018 -0400 +++ b/test-data/bam_to_sam_out2.sam Tue Sep 28 16:10:41 2021 +0000 |
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| @@ -4,3 +4,4 @@ @SQ SN:chr8 LN:202 @RG ID:0 SM:Hi,Mom! @PG ID:1 PN:Hey! VN:2.0 +@PG ID:samtools PN:samtools PP:1 VN:1.12 CL:samtools view -o /tmp/tmpl_eh5cxt/files/3/0/2/dataset_3025757e-159d-4ced-a398-2d7dc823e34b.dat -H /tmp/tmpl_eh5cxt/files/9/5/d/dataset_95dbe51c-ade9-4f37-9399-79ec158c1516.dat |