| Previous changeset 1:6ade12d94f9a (2018-09-25) Next changeset 3:b91e0f76afe9 (2018-10-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8 |
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modified:
macros.xml samtools_view.xml |
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added:
test-data/test_ds.bam test-data/test_ds.cram test-data/test_ds.sam |
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| diff -r 6ade12d94f9a -r 02afb5ea2fce macros.xml --- a/macros.xml Tue Sep 25 04:21:24 2018 -0400 +++ b/macros.xml Thu Sep 27 08:51:16 2018 -0400 |
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| @@ -74,6 +74,9 @@ 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." /> + </xml> <xml name="flag_options"> <option value="1">read is paired</option> <option value="2">read is mapped in a proper pair</option> |
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| diff -r 6ade12d94f9a -r 02afb5ea2fce samtools_view.xml --- a/samtools_view.xml Tue Sep 25 04:21:24 2018 -0400 +++ b/samtools_view.xml Thu Sep 27 08:51:16 2018 -0400 |
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| @@ -3,7 +3,9 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package">gawk</requirement> + </expand> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @@ -11,7 +13,19 @@ ## prepare reference data @PREPARE_FASTA_IDX@ @PREPARE_IDX@ - + #if $cond_subsample.select_subsample == 'target': + ##this must be done before the main command because we don't know the total # reads until execution time + #if str($cond_subsample.seed) == '': + #set seed_expr="int(rand() * 32768)" + #else + #set seed_expr=$cond_subsample.seed + #end if + #if $input.is_of_type('sam'): + sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` && + #else + sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` && + #end if + #end if ##call samtools view samtools view -@ \$addthreads @@ -62,12 +76,17 @@ -x '${s.readtag}' #end for #end if - #if $cond_subsample.select_subsample == 'yes': - #set fraction=str($cond_subsample.subsample).split('.')[1] - #if str($cond_subsample.seed) == '': - -s "\${RANDOM}".$fraction + #if $cond_subsample.select_subsample != 'no': + #if $cond_subsample.select_subsample == "target": + ##this is calculated at execution time before the main samtools command + "\${sample_fragment}" #else - -s $cond_subsample.seed.$fraction + #set fraction=str($cond_subsample.fraction).split('.')[1] + #if str($cond_subsample.seed) == '': + -s "\${RANDOM}".$fraction + #else + -s $cond_subsample.seed.$fraction + #end if #end if #end if @@ -181,12 +200,17 @@ </conditional> <conditional name="cond_subsample"> <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> + <option value="fraction">Specify a fraction to keep</option> + <option value="target">Specify a target # of reads</option> + <option value="no" selected="True">No downsampling</option> </param> - <when value="yes"> - <param name="subsample" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." /> - <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> + <when value="fraction"> + <param name="fraction" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." /> + <expand macro="seed_input" /> + </when> + <when value='target'> + <param name="target" type="integer" optional="False" value="" min="0" label="Target # of reads" help="sets the target number of reads to subsample." /> + <expand macro="seed_input" /> </when> <when value="no"/> </conditional> @@ -383,6 +407,46 @@ </conditional> <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" /> </test> + <!-- sampling options--> + <test> + <param name="input" value="test.sam" ftype="sam" /> + <param name="outtype" value="sam" /> + <conditional name="cond_subsample"> + <param name="select_subsample" value="target" /> + <param name="target" value="2" /> + </conditional> + <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> + </test> + <test> + <param name="input" value="test.sam" ftype="sam" /> + <param name="outtype" value="sam" /> + <conditional name="cond_subsample"> + <param name="select_subsample" value="target" /> + <param name="seed" value="7" /> + <param name="target" value="2" /> + </conditional> + <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" /> + </test> + <test> + <param name="input" value="test.bam" ftype="bam" /> + <param name="outtype" value="bam" /> + <conditional name="cond_subsample"> + <param name="select_subsample" value="target" /> + <param name="seed" value="7" /> + <param name="target" value="2" /> + </conditional> + <output name="outputsam" file="test_ds.bam" ftype="bam" /> + </test> + <test> + <param name="input" value="test.bam" ftype="bam" /> + <param name="outtype" value="bam" /> + <conditional name="cond_subsample"> + <param name="select_subsample" value="fraction" /> + <param name="seed" value="7" /> + <param name="fraction" value=".2" /> + </conditional> + <output name="outputsam" file="test_ds.bam" ftype="bam" /> + </test> </tests> <help> **What it does** |
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| diff -r 6ade12d94f9a -r 02afb5ea2fce test-data/test_ds.bam |
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| Binary file test-data/test_ds.bam has changed |
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| diff -r 6ade12d94f9a -r 02afb5ea2fce test-data/test_ds.cram |
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| Binary file test-data/test_ds.cram has changed |
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| diff -r 6ade12d94f9a -r 02afb5ea2fce test-data/test_ds.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_ds.sam Thu Sep 27 08:51:16 2018 -0400 |
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| @@ -0,0 +1,8 @@ +@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 +SRR065390.6023338 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 |