Mercurial > repos > iuc > samtools_markdup
annotate samtools_markdup.xml @ 6:b5527cc104ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 5cb103832529f17e5c72e7f122758c13519fbe5e
| author | iuc |
|---|---|
| date | Mon, 15 Aug 2022 09:17:57 +0000 |
| parents | 887e02a45734 |
| children | ce32171c6d44 |
| rev | line source |
|---|---|
|
6
b5527cc104ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
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changeset
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1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" > |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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2 <description>marks duplicate alignments</description> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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3 <macros> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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4 <import>macros.xml</import> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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5 </macros> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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6 <expand macro="requirements"/> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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7 <expand macro="stdio"/> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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8 <expand macro="version_command"/> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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9 <command><![CDATA[ |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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10 @ADDTHREADS@ |
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3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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11 ## coordinate sort input |
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0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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12 #if not $bamfile.is_of_type('bam'): |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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13 samtools sort |
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1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" |
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0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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15 -O sam |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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16 -o coordsort.sam |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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17 '$bamfile' && |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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18 #else: |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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19 ln -s '$bamfile' coordsort.sam && |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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20 #end if |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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21 |
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5
887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
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22 ## copy fasta reference if needed |
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887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
parents:
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23 ## because samtools will try to write a .fai file next to it |
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887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
parents:
4
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24 #if $output_options.output_format.select_oformat == "CRAM" |
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887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
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25 ln -s '$output_options.output_format.ref_file' ref_file.fa && |
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887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
parents:
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26 #end if |
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887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
iuc
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27 |
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3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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28 samtools markdup |
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0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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29 |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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30 -@ \$addthreads |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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31 #if str($maxlen) != '': |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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32 -l $maxlen |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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33 #end if |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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34 $remove |
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0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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35 $supp |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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36 #if $odist: |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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37 -d $odist |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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38 #end if |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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39 $existing_tags |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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40 -m $mode |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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41 $include_fails |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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42 #if $output_options.stats == 'yes' |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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43 -s |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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44 -f '$stats_output' |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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45 #end if |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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46 -O $output_options.output_format.select_oformat |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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47 #if $output_options.output_format.select_oformat == "CRAM" |
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5
887e02a45734
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 84db51c96845854eb42c1a9949e4b79316b41925
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48 --reference ref_file.fa |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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49 #end if |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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50 coordsort.sam |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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51 '$output' |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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52 ]]></command> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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53 <inputs> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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54 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" /> |
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046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
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55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" /> |
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1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
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56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." /> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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60 <param argument="--mode" type="select" label="Duplicate decision method for paired reads."> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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61 <option selected="true" value="t">(t) measure positions based on template start/end.</option> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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62 <option value="s">(s) measure positions based on sequence start. </option> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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63 </param> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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64 <param argument="--include-fails" type="boolean" truevalue="--include-fails" falsevalue="" label="Include quality check failed reads." /> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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65 <section name="output_options" title="Output Options" expanded="true"> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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66 <param name="stats" type="select" argument="-s" label="Print basic statistics"> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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67 <option value="yes">Yes</option> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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68 <option value="no" selected="True">No</option> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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69 </param> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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70 <conditional name="output_format"> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
71 <param name="select_oformat" type="select" label="Output format" help="Specify output format"> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
72 <option value="SAM">SAM</option> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
73 <option value="BAM" selected="True">BAM</option> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
74 <option value="CRAM">CRAM</option> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
75 </param> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
76 <when value="SAM" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
77 <when value="BAM" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
78 <when value="CRAM"> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
79 <param name="ref_file" type="data" format="fasta" label="Reference FASTA file" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
80 </when> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
81 </conditional> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
82 </section> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
83 </inputs> |
|
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
84 <outputs> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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|
85 <!-- output bam, if input was name sorted then restore this sorting order --> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
86 <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}"> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
87 <change_format> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
88 <when input="output_format.select_oformat" value="SAM" format="sam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
89 <when input="output_format.select_oformat" value="BAM" format="bam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
90 <when input="output_format.select_oformat" value="CRAM" format="cram" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
91 </change_format> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
92 </data> |
|
2
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
93 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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94 <filter>(output_options['stats'] == 'yes')</filter> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
parents:
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changeset
|
95 </data> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
96 </outputs> |
|
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
97 <tests> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
98 <!-- 1) --> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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|
99 <test expect_num_outputs="1"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
100 <param name="bamfile" value="1_markdup.sam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
101 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
102 </test> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
103 <!-- 2) --> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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|
104 <test expect_num_outputs="1"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
105 <param name="bamfile" value="2_remove_dups.sam" /> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
106 <param name="remove" value="-r" /> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" /> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
108 </test> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
109 <!-- 3) --> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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|
110 <test expect_num_outputs="1"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
111 <param name="bamfile" value="3_mark_supp_dup.bam" /> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
112 <param name="supp" value="-S" /> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" /> |
|
0
046cbf29795a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
iuc
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|
114 </test> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
115 <!-- 4) test stats output --> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
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|
116 <test expect_num_outputs="2"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
117 <param name="bamfile" value="1_markdup.sam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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118 <param name="stats" value="yes" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
119 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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120 <output name="stats_output" file="stats.txt" lines_diff="2" /> |
|
1
83b8e36e9cbe
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"
iuc
parents:
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|
121 </test> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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122 <!-- 5) check that stderr is not swallowed w test data from fixmate --> |
|
2
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
123 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true"> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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124 <param name="bamfile" value="3_two_read_mapped.sam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
125 <param name="stats" value="yes"/> |
|
2
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
parents:
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|
126 <!-- for some reason this is not possible at the moment |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
127 <output name="stats_output"> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
128 <assert_contents> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
129 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
130 </assert_contents> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
131 </output> --> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
132 <assert_stderr> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
parents:
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|
133 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
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|
134 </assert_stderr> |
|
a312a0fdaf31
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit e33502c1fc025859ccbcd2a273f837fac9d322e0"
iuc
parents:
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|
135 </test> |
|
3
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
136 <!-- 6) check optical distance and check -c option --> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
137 <test expect_num_outputs="1"> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
138 <param name="bamfile" value="1_markdup.sam" /> |
|
d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
139 <param name="odist" value="10" /> |
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d0a568e1904b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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140 <param name="existing_tags" value="-c" /> |
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141 <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" /> |
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142 </test> |
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143 <!-- 7) check new mode s --> |
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144 <test expect_num_outputs="1"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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145 <param name="bamfile" value="1_markdup.sam" /> |
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146 <param name="mode" value="s" /> |
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147 <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" /> |
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148 </test> |
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149 <!-- 8) check include-fails --> |
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150 <test expect_num_outputs="1"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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151 <param name="bamfile" value="1_markdup.sam" /> |
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152 <param name="include_fails" value="true" /> |
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153 <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" /> |
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154 </test> |
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155 <!-- 9) test sam format --> |
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156 <test expect_num_outputs="1"> |
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157 <param name="bamfile" value="1_markdup.sam" /> |
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158 <param name="select_oformat" value="SAM" /> |
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159 <output name="output" file="9_markdup.expected.sam" lines_diff="4" /> |
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160 </test> |
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161 <!-- 10) test cram format --> |
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162 <test expect_num_outputs="1"> |
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163 <param name="bamfile" value="10_markdup.sam" /> |
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164 <param name="select_oformat" value="CRAM" /> |
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165 <param name="ref_file" value="test.fa" /> |
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166 <output name="output" file="10_markdup.expected.cram" compare="sim_size" delta="250"/> |
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167 </test> |
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168 </tests> |
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169 <help> |
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170 Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides. |
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171 |
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172 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted. |
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173 The output is BAM (which is query name sorted again if the input is). |
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174 |
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175 The optional basic statistics output of samtools markdup can be visualized with MultiQC. |
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176 |
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177 </help> |
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178 <expand macro="citations"/> |
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179 </tool> |