| Previous changeset 7:b01db2684fa5 (2020-01-21) Next changeset 9:b72793637686 (2021-01-04) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346" |
|
modified:
samtools_view.xml |
|
added:
test-data/no_reads.bam test-data/no_reads.sam |
| b |
| diff -r b01db2684fa5 -r bf328cec6a42 samtools_view.xml --- a/samtools_view.xml Tue Jan 21 07:40:18 2020 -0500 +++ b/samtools_view.xml Wed Sep 02 15:29:22 2020 -0400 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy1">\n+<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2">\n <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>\n <macros>\n <import>macros.xml</import>\n@@ -20,21 +20,19 @@\n </xml>\n <xml name="output_format_selector">\n <conditional name="output_format">\n- <param name="oformat" type="select" label="Output format">\n+ <param name="oformat" type="select" label="Output format"\n+ help="Note on BAM output format: The tool will generate coordinate-sorted BAM, i.e., may change the order of reads compared to the input. For BAM input, select \'Same as input\' to produce BAM output with the read order retained.">\n+ <option value="input">Same as input</option>\n <option value="sam">SAM</option>\n <option value="bam" selected="True">BAM (-b)</option>\n <option value="cram">CRAM (-C)</option>\n </param>\n+ <when value="input" />\n <when value="sam">\n <yield />\n- <param name="fmtopt" type="hidden" value="" />\n </when>\n- <when value="bam">\n- <param name="fmtopt" type="hidden" value="-b" />\n- </when>\n- <when value="cram">\n- <param name="fmtopt" type="hidden" value="-C" />\n- </when>\n+ <when value="bam" />\n+ <when value="cram" />\n </conditional>\n </xml>\n </macros>\n@@ -49,10 +47,35 @@\n @PREPARE_FASTA_IDX@\n @PREPARE_IDX@\n \n+ ## determine the output format flag to pass to samtools view\n+ ## -c for count mode\n+ ## -b to produce BAM-formatted output\n+ ## -C to produce CRAM-formatted output\n+ ## SAM is the default ouput format\n+ #set $fmtopt = \'\'\n+ #if str($mode.output_options.reads_report_type) == \'count\':\n+ #set $fmtopt = \'-c\'\n+ #else:\n+ #if str($mode.output_options.output_format.oformat) == \'bam\':\n+ #set $fmtopt = \'-b\'\n+ #elif str($mode.output_options.output_format.oformat) == \'cram\':\n+ #set $fmtopt = \'-C\'\n+ #elif str($mode.output_options.output_format.oformat) == \'input\':\n+ #if $input.is_of_type(\'bam\'):\n+ #set $fmtopt = \'-b\'\n+ #elif $input.is_of_type(\'cram\'):\n+ #set $fmtopt = \'-C\'\n+ #else:\n+ ## input in SAM format, make sure to keep header if present\n+ #set $fmtopt = \'-h\'\n+ #end if\n+ #end if\n+ #end if\n+\n #if str($mode.outtype) == \'header\':\n ## call samtools view and be done\n samtools view\n- -H ${mode.output_options.output_format.fmtopt} -o outfile\n+ -H $fmtopt -o outfile\n @REF_DATA@\n infile\n #else:\n@@ -130,11 +153,11 @@\n ## not dealing with all of the reads in the indexed\n ## file. We have to do an extra pass over the input to\n ## count the reads to subsample.\n- sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk \'{s=\\$1} END {frac=${mode.subsample_config.subsampling_mode.target}/s; print(frac < 1 ? $seed+frac : ".0")}\'` &&\n+ sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk \'{s=\\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}\'` &&\n #else:\n ## We can get the count of reads to subsample using\n ## an inexpensive call to idxstats.\n- '..b'ile="test.sam" ftype="sam" />\n </test>\n <test>\n+ <!-- subsampling SAM input without reads -->\n+ <param name="input" value="no_reads.sam" ftype="sam" />\n+ <conditional name="mode">\n+ <param name="outtype" value="selected_reads" />\n+ <section name="subsample_config">\n+ <conditional name="subsampling_mode">\n+ <param name="select_subsample" value="target" />\n+ <param name="target" value="20" />\n+ </conditional>\n+ </section>\n+ <conditional name="output_options">\n+ <conditional name="output_format">\n+ <param name="oformat" value="input" />\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="outputsam" file="no_reads.sam" ftype="sam" />\n+ </test>\n+ <test>\n+ <!-- subsampling BAM input without reads -->\n+ <param name="input" value="no_reads.bam" ftype="bam" />\n+ <conditional name="mode">\n+ <param name="outtype" value="selected_reads" />\n+ <section name="subsample_config">\n+ <conditional name="subsampling_mode">\n+ <param name="select_subsample" value="target" />\n+ <param name="target" value="20" />\n+ </conditional>\n+ </section>\n+ <conditional name="output_options">\n+ <conditional name="output_format">\n+ <param name="oformat" value="input" />\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <output name="outputsam" file="no_reads.bam" ftype="bam" />\n+ </test>\n+ <test>\n <param name="input" value="test.sam" ftype="sam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -653,7 +785,7 @@\n </section>\n <conditional name="output_options">\n <conditional name="output_format">\n- <param name="oformat" value="sam" />\n+ <param name="oformat" value="input" />\n </conditional>\n </conditional>\n </conditional>\n@@ -672,7 +804,7 @@\n </section>\n <conditional name="output_options">\n <conditional name="output_format">\n- <param name="oformat" value="bam" />\n+ <param name="oformat" value="input" />\n </conditional>\n </conditional>\n </conditional>\n@@ -691,7 +823,7 @@\n </section>\n <conditional name="output_options">\n <conditional name="output_format">\n- <param name="oformat" value="bam" />\n+ <param name="oformat" value="input" />\n </conditional>\n </conditional>\n </conditional>\n@@ -710,7 +842,7 @@\n </section>\n <conditional name="output_options">\n <conditional name="output_format">\n- <param name="oformat" value="bam" />\n+ <param name="oformat" value="input" />\n </conditional>\n </conditional>\n </conditional>\n@@ -730,7 +862,7 @@\n <conditional name="output_options">\n <param name="reads_report_type" value="dropped" />\n <conditional name="output_format">\n- <param name="oformat" value="bam" />\n+ <param name="oformat" value="input" />\n </conditional>\n </conditional>\n </conditional>\n' |
| b |
| diff -r b01db2684fa5 -r bf328cec6a42 test-data/no_reads.bam |
| b |
| Binary file test-data/no_reads.bam has changed |
| b |
| diff -r b01db2684fa5 -r bf328cec6a42 test-data/no_reads.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/no_reads.sam Wed Sep 02 15:29:22 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +@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 |