| Previous changeset 14:5826298f6a73 (2022-08-15) Next changeset 16:2dce91e11ca7 (2024-08-30) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a |
|
modified:
macros.xml samtools_view.xml |
| b |
| diff -r 5826298f6a73 -r 6be888be75f9 macros.xml --- a/macros.xml Mon Aug 15 09:19:43 2022 +0000 +++ b/macros.xml Mon Nov 20 22:17:43 2023 +0000 |
| [ |
| @@ -5,7 +5,14 @@ <yield/> </requirements> </xml> + <!-- NOTE: for some tools only the version of the requirement but not the + tool's version is controlled by the TOOL_VERSION token + (because their version is ahead of the requirement version .. + please only bump the minor version in order to let the requirement + version catch up eventually). To find the tools check: + `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> <token name="@TOOL_VERSION@">1.15.1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">20.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 @@ -212,37 +219,7 @@ <xml name="citations"> <citations> - <citation type="bibtex"> - @misc{SAM_def, - title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/},} - </citation> - <citation type="doi">10.1093/bioinformatics/btp352</citation> - <citation type="doi">10.1093/bioinformatics/btr076</citation> - <citation type="doi">10.1093/bioinformatics/btr509</citation> - <citation type="bibtex"> - @misc{Danecek_et_al, - Author={Danecek, P., Schiffels, S., Durbin, R.}, - title={Multiallelic calling model in bcftools (-m)}, - url = {http://samtools.github.io/bcftools/call-m.pdf},} - </citation> - <citation type="bibtex"> - @misc{Durbin_VCQC, - Author={Durbin, R.}, - title={Segregation based metric for variant call QC}, - url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} - </citation> - <citation type="bibtex"> - @misc{Li_SamMath, - Author={Li, H.}, - title={Mathematical Notes on SAMtools Algorithms}, - url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} - </citation> - <citation type="bibtex"> - @misc{SamTools_github, - title={SAMTools GitHub page}, - url = {https://github.com/samtools/samtools},} - </citation> + <citation type="doi">10.1093/gigascience/giab008</citation> </citations> </xml> <xml name="version_command"> |
| b |
| diff -r 5826298f6a73 -r 6be888be75f9 samtools_view.xml --- a/samtools_view.xml Mon Aug 15 09:19:43 2022 +0000 +++ b/samtools_view.xml Mon Nov 20 22:17:43 2023 +0000 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">\n+<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>\n <macros>\n <import>macros.xml</import>\n@@ -154,11 +154,11 @@\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=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\\n", frac > 1 ? $seed+1/frac : ".0")}\'` &&\n+ sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk \'{s=\\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\\n", fac > 1 ? 1/fac : 1)}\'` &&\n #else:\n ## We can get the count of reads to subsample using\n ## an inexpensive call to idxstats.\n- sample_fragment=`samtools idxstats infile | awk \'{s+=\\$4+\\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\\n", frac > 1 ? $seed+1/frac : ".0")}\'` &&\n+ sample_fragment=`samtools idxstats infile | awk \'{s+=\\$4+\\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\\n", fac > 1 ? 1/fac : 1)}\'` &&\n #end if\n #end if\n #end if\n@@ -172,12 +172,13 @@\n $std_filters\n \n #if $with_subsampling:\n+ --subsample-seed $seed\n #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":\n ##this is calculated at execution time before the main samtools command\n- -s \\${sample_fragment}\n+ --subsample \\${sample_fragment}\n #else:\n- #set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor)\n- -s $fraction\n+ #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor)\n+ --subsample $fraction\n #end if\n #end if\n \n@@ -398,13 +399,13 @@\n </data>\n </outputs>\n <tests>\n-<!-- 1) sam to bam (copied from the sam_to_bam tool) -->\n- <test>\n+ <!-- 1) sam to bam (copied from the sam_to_bam tool) -->\n+ <test expect_num_outputs="1">\n <param name="input" ftype="sam" value="in_test_1.sam" />\n <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" />\n </test>\n <!-- 2) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="cached" />\n@@ -413,7 +414,7 @@\n <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" />\n </test>\n <!-- 3) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" ftype="sam" value="in_test_3.sam" />\n <conditional name="addref_cond">\n <param name="addref_select" value="history" />\n@@ -422,7 +423,7 @@\n <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" />\n </test>\n <!-- 4) cram to bam -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_4.cram" ftype="cram" />\n <conditional name="addref_cond">\n <param name="addref_select" value="history" />\n@@ -431,7 +432,7 @@\n <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff='..b' name="input" value="in_test_15.sam" ftype="sam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -710,7 +711,7 @@\n <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />\n </test>\n <!-- 22) target > total reads -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_15.sam" ftype="sam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -729,7 +730,7 @@\n <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/>\n </test>\n <!-- 23) -->\n- <test>\n+ <test expect_num_outputs="1">\n <!-- subsampling SAM input without reads -->\n <param name="input" value="in_test_23.sam" ftype="sam" />\n <conditional name="mode">\n@@ -749,7 +750,7 @@\n <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/>\n </test>\n <!-- 24) -->\n- <test>\n+ <test expect_num_outputs="1">\n <!-- subsampling BAM input without reads -->\n <param name="input" value="in_test_24.bam" ftype="bam" />\n <conditional name="mode">\n@@ -769,7 +770,7 @@\n <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" />\n </test>\n <!-- 25) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_15.sam" ftype="sam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -789,7 +790,7 @@\n <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />\n </test>\n <!-- 26) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_14.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -809,7 +810,7 @@\n <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" />\n </test>\n <!-- 27) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_14.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -829,7 +830,7 @@\n <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/>\n </test>\n <!-- 28) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_14.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -849,7 +850,7 @@\n <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" />\n </test>\n <!-- 29) -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_14.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -870,7 +871,7 @@\n <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/>\n </test>\n <!-- 30) testing tag filtering -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_30.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n@@ -889,7 +890,7 @@\n <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" />\n </test>\n <!-- 31) testing readname filtering -->\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input" value="in_test_30.bam" ftype="bam" />\n <conditional name="mode">\n <param name="outtype" value="selected_reads" />\n' |