Mercurial > repos > avowinkel > gatk
comparison print_reads.xml @ 0:b80ff7f43ad1 draft default tip
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/gatk commit 8764cef47529f6285678af4ca24b66d0fe516b88-dirty
| author | avowinkel |
|---|---|
| date | Thu, 24 Sep 2015 12:10:01 -0400 |
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| children |
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| -1:000000000000 | 0:b80ff7f43ad1 |
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| 1 <macros> | |
| 2 <xml name="PrintReadsParameters" tokens="tag"> | |
| 3 | |
| 4 <expand macro="macro_bam_input" tag="@TAG@" /> | |
| 5 | |
| 6 <!-- BQSR in main config --> | |
| 7 | |
| 8 <expand macro="macro_optional_parameters"> | |
| 9 | |
| 10 <param name="number" type="integer" value="" optional="true" label="Print the first n reads from the file, discarding the rest" help="-n,‑‑number &lt;number&gt;" /> | |
| 11 | |
| 12 <param name="platform" type="text" value="" optional="true" label="Exclude all reads with this platform from the output" help="-platform,‑‑platform &lt;platform&gt;" /> | |
| 13 | |
| 14 <param name="readGroup" type="text" value="" optional="true" label="Exclude all reads with this read group from the output" help="-readGroup,‑‑readGroup &lt;readGroup&gt;" /> | |
| 15 | |
| 16 <param name="sample_file" type="data" format="txt" optional="true" label="File containing a list of samples (one per line). Can be specified multiple times" help="-sf,‑‑sample_file &lt;sample_file&gt;" /> | |
| 17 | |
| 18 <repeat name="sample_names" title="Sample names to be included in the analysis" help="-sn,‑‑sample_name &lt;sample_name&gt;"> | |
| 19 <param name="sample_name" type="text" value="" title="Sample name to be included in the analysis" /> | |
| 20 </repeat> | |
| 21 | |
| 22 <param name="simplify" type="text" truevalue="-s" falsevalue="" label="Erase all extra attributes in the read but keep the read group information" help="-s,‑‑simplify" /> | |
| 23 | |
| 24 </expand> | |
| 25 | |
| 26 </xml> | |
| 27 | |
| 28 <xml name="PrintReadsOutput"> | |
| 29 <data format="bam" name="pr_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)"> | |
| 30 <yield /> | |
| 31 </data> | |
| 32 </xml> | |
| 33 | |
| 34 <template name="PrintReadsPreprocessing"> | |
| 35 <![CDATA[ | |
| 36 @token_bam_input_pre@ | |
| 37 ]]> | |
| 38 </template> | |
| 39 | |
| 40 <template name="PrintReadsOptions"> | |
| 41 <![CDATA[ | |
| 42 --out ${pr_output_bam} | |
| 43 | |
| 44 @token_bam_input@ | |
| 45 | |
| 46 #set $optionals = $analysis_type.optional_parameters | |
| 47 #if $optionals.optional_parameters_enabled | |
| 48 #if int($optionals.number) > 0 | |
| 49 --number $optionals.number | |
| 50 #end if | |
| 51 #if str($optionals.platform) | |
| 52 --platform $optionals.platform | |
| 53 #end if | |
| 54 #if str($optionals.readGroup) | |
| 55 --readGroup $optionals.readGroup | |
| 56 #end if | |
| 57 #if $optionals.sample_file | |
| 58 --sample_file $optionals.sample_file | |
| 59 #end if | |
| 60 #if $optionals.sample_names | |
| 61 #for $sample in $optionals.sample_names: | |
| 62 --intervals ${sample.sample_name} | |
| 63 #end for | |
| 64 #end if | |
| 65 $optionals.simplify | |
| 66 #end if | |
| 67 ]]> | |
| 68 </template> | |
| 69 </macros> | |
| 70 | |
| 71 |