Mercurial > repos > iuc > samtools_view
annotate samtools_view.xml @ 3:097c44aaf6d4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
| author | iuc |
|---|---|
| date | Tue, 20 Nov 2018 06:19:49 -0500 |
| parents | 80d8ca44f8da |
| children | f2b321f691e4 |
| rev | line source |
|---|---|
|
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@"> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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2 <description>reformat, filter, or subsample</description> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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3 <macros> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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5 </macros> |
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2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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6 <expand macro="requirements"> |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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7 <requirement type="package">gawk</requirement> |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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8 </expand> |
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0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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9 <expand macro="stdio"/> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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10 <expand macro="version_command"/> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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11 <command><![CDATA[ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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12 @ADDTHREADS@ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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13 ## prepare reference data |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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14 @PREPARE_FASTA_IDX@ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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15 @PREPARE_IDX@ |
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2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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16 #if $cond_subsample.select_subsample == 'target': |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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17 ##this must be done before the main command because we don't know the total # reads until execution time |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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changeset
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18 #if str($cond_subsample.seed) == '': |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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changeset
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19 #set seed_expr="int(rand() * 32768)" |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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changeset
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20 #else |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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changeset
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21 #set seed_expr=$cond_subsample.seed |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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changeset
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22 #end if |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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23 #if $input.is_of_type('sam'): |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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24 sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` && |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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25 #else |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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26 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` && |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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changeset
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27 #end if |
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80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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28 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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29 ##call samtools view |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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30 samtools view |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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31 -@ \$addthreads |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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32 |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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33 #if $outtype == 'count': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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34 -c |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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35 #elif $outtype == 'bam': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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36 -b |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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37 #elif $outtype == 'cram': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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38 -C |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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39 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
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40 |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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41 ## filter options (regions filter is the last parameter) |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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42 #if $cond_filter.select_filter == 'yes': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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43 #if $cond_filter.cond_region.select_region == 'bed' and str( $cond_filter.cond_region.bedfile ) != 'None' |
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3
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
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44 -L '$cond_filter.cond_region.bedfile' |
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0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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45 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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46 #if $cond_filter.cond_rg.select_rg == 'text': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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47 -r '$cond_filter.cond_rg.readgr' |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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48 #else if $cond_filter.cond_rg.select_rg == 'file': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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49 -R '$cond_filter.cond_rg.rgfile' |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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50 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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51 #if str($cond_filter.quality) != '' and int( $cond_filter.quality ) > 0 |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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52 -q $cond_filter.quality |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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53 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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54 #if str( $cond_filter.library ) != '' |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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55 -l '$cond_filter.library' |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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56 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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57 #if str( $cond_filter.cigarcons ) != '' |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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58 -m $cond_filter.cigarcons |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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59 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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60 #if str($cond_filter.inclusive_filter) != 'None': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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61 #set $filter = $cond_filter.inclusive_filter |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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62 @FLAGS@ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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63 -f $flags |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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64 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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65 #if str($cond_filter.exclusive_filter) != 'None': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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66 #set $filter = $cond_filter.exclusive_filter |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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67 @FLAGS@ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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68 -F $flags |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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69 #end if |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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70 #if str($cond_filter.exclusive_filter_all) != 'None': |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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71 #set $filter = $cond_filter.exclusive_filter_all |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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72 @FLAGS@ |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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73 -G $flags |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
74 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
75 #for $i, $s in enumerate($cond_filter.readtags) |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
76 -x '${s.readtag}' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
77 #end for |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
78 #end if |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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diff
changeset
|
79 #if $cond_subsample.select_subsample != 'no': |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
80 #if $cond_subsample.select_subsample == "target": |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
81 ##this is calculated at execution time before the main samtools command |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
82 "\${sample_fragment}" |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
83 #else |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
84 #set fraction=str($cond_subsample.fraction).split('.')[1] |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
85 #if str($cond_subsample.seed) == '': |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
86 -s "\${RANDOM}".$fraction |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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diff
changeset
|
87 #else |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
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diff
changeset
|
88 -s $cond_subsample.seed.$fraction |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
89 #end if |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
90 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
91 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
92 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
93 ## output options |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
94 $adv_output.header |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
95 $adv_output.collapsecigar |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
96 #if $adv_output.outputpassing == 'yes' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
97 -U inv_outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
98 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
99 -o outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
100 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
101 ## additional reference data |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
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102 #if $reffa!=None: |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
103 -T '$reffa' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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104 -t '$reffai' |
|
1
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
parents:
0
diff
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|
105 #end if |
|
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
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|
106 |
|
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
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diff
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|
107 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963) |
|
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
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|
108 #if $outtype=='cram': |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
|
109 --output-fmt-option no_ref |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
110 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
111 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
112 infile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
113 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
114 ## region filter need to be at the end |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
115 #if $cond_filter.select_filter == 'yes' and $cond_filter.cond_region.select_region == 'text': |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
116 '$cond_filter.cond_region.regions' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
117 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
118 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
|
120 ## then sort the output by coordinate, |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
121 #if not $input.is_of_type('bam') and $outtype == 'bam': |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
122 && samtools sort |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
124 -O bam |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
125 -o 'tmpsam' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
126 outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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|
127 && mv tmpsam outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
|
128 #if $adv_output.outputpassing == 'yes': |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
129 && samtools sort |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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|
130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
131 -O bam |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
132 -o 'tmpsam' |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
133 inv_outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
134 && mv tmpsam inv_outfile |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
135 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
136 #end if |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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|
137 ]]></command> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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|
138 <inputs> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
139 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) --> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
140 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
141 <param name="outtype" type="select" argument="-b/-C/-c" label="Output type"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
142 <help>Select output type. In case of counts only the total number of alignments is returned. All filters are taken into account</help> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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|
143 <option value="sam">SAM</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
144 <option value="bam">BAM (-b)</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
145 <option value="cram">CRAM (-C)</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
146 <option value="count">Count of alignments (-c)</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
147 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
148 <conditional name="cond_filter"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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|
149 <param name="select_filter" type="select" label="Filter alignment"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
150 <option value="yes">Yes</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
151 <option value="no" selected="True">No</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
152 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
153 <when value="yes"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
154 <conditional name="cond_region"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
155 <param name="select_region" type="select" label="Filter by regions"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff
changeset
|
156 <option value="no" selected="True">No</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
157 <option value="text">Manualy specify regions</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
158 <option value="bed">Regions from BED file</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
159 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
160 <when value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
161 <when value="text"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
162 <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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163 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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164 <when value="bed"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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165 <param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
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166 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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167 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
168 <conditional name="cond_rg"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
169 <param name="select_rg" type="select" label="Filter by readgroup"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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170 <option value="no" selected="True">No</option> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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171 <option value="text">Single read group </option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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172 <option value="file">Read groups from file</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
173 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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174 <when value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
175 <when value="text"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
176 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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177 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
178 <when value="file"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
179 <param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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180 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
181 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
182 <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
183 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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184 <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
185 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
186 <expand macro="flag_options" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
187 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
188 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
189 <expand macro="flag_options" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
190 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
191 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
192 <expand macro="flag_options" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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193 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
194 <!-- TODO could also make this a text field (comma/space separated) --> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
195 <repeat name="readtags" title="Filter by read tags"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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196 <param name="readtag" type="text" argument="-x" label="Filter by read tag" help="Read tag to exclude from output."/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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197 </repeat> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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198 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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199 <when value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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200 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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201 <conditional name="cond_subsample"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
202 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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203 <option value="fraction">Specify a fraction to keep</option> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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204 <option value="target">Specify a target # of reads</option> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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205 <option value="no" selected="True">No downsampling</option> |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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206 </param> |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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changeset
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207 <when value="fraction"> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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208 <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." /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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209 <expand macro="seed_input" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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210 </when> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
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1
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changeset
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211 <when value='target'> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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212 <param name="target" type="integer" optional="False" value="" min="0" label="Target # of reads" help="sets the target number of reads to subsample." /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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|
213 <expand macro="seed_input" /> |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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214 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
215 <when value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
216 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
217 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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218 <param name="addref_select" type="select" label="Reference data"> |
|
1
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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0
diff
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|
219 <help>Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help).</help> |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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220 <option value="no" selected="True">No, see help (-output-fmt-option no_ref)</option> |
|
1
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
iuc
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221 <option value="history">Use a genome/index from the history (-t/-T)</option> |
|
390fc279c3e5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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0
diff
changeset
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222 <option value="cached">Use a built-in genome (-t/-T)</option> |
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0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
223 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
224 <when value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
225 <when value="history"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
226 <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
227 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
228 <when value="cached"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
229 <param name="ref" type="select" label="Using reference genome"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff
changeset
|
230 <options from_data_table="fasta_indexes"> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff
changeset
|
231 <filter column="1" key="dbkey" ref="input" type="data_meta" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
232 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
233 </options> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
234 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
|
235 </when> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
236 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
237 <section name="adv_output" title="Output Options" expanded="false"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
diff
changeset
|
238 <param name="header" type="select" argument="-h/-H" label="Header options"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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239 <option value="-h" selected="True">Include header in SAM output (-h)</option> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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diff
changeset
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240 <option value="-H">Return header only (-H)</option> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
241 <option value="">Exclude header</option> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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242 </param> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
243 <param name="outputpassing" type="boolean" argument="-U" truevalue="yes" falsevalue="no" checked="false" label="Output alignments not passing the filter" help="Write alignments that are not selected by the various filter options to an extra data set. When this option is used, all alignments (or all alignments intersecting the regions specified) are written to either the output data set or this extra output data set, but never both." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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244 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
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245 </section> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
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246 </inputs> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
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247 <outputs> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
|
248 <!-- TODO do I need an action for dbkey? --> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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249 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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250 <filter>outtype != 'count'</filter> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
251 <!-- TODO is change_format deprecated? how can I modify the type for the different bam types? --> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
252 <change_format> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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253 <when input="outtype" value="sam" format="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
254 <when input="outtype" value="bam" format="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
255 <when input="outtype" value="cram" format="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
256 </change_format> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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257 </data> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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258 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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259 <filter>adv_output['outputpassing'] == 'yes' and outtype != 'count'</filter> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
260 <change_format> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
261 <when input="outtype" value="sam" format="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
262 <when input="outtype" value="bam" format="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
263 <when input="outtype" value="cram" format="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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264 </change_format> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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changeset
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265 </data> |
|
3
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
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266 <data name="outputcnt" format="txt" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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267 <filter>outtype == 'count'</filter> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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268 </data> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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269 </outputs> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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270 <tests> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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271 <!-- sam to bam (copied from the sam_to_bam tool) --> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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272 <test> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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273 <param name="input" ftype="sam" value="sam_to_bam_in1.sam" /> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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274 <param name="outtype" value="bam" /> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
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275 <conditional name="addref_cond"> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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276 <param name="addref_select" value="history" /> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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277 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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278 </conditional> |
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5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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279 <output name="outputsam" ftype="bam" file="sam_to_bam_out1.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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280 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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281 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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282 <param name="input" ftype="sam" dbkey="equCab2" value="sam_to_bam_in1.sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
283 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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284 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
285 <param name="addref_select" value="cached" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
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286 <param name="ref" value="equCab2chrM" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
287 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
288 <output name="outputsam" ftype="bam" file="sam_to_bam_out2.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
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289 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
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290 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
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291 <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
292 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
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293 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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294 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
295 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
296 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
297 <output name="outputsam" ftype="bam" file="sam_to_bam_out3.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
298 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
299 <!-- bam to cram + region filter (adapted from bam_to_cram tool)--> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
300 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
301 <param name="input" value="test.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
302 <param name="outtype" value="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
303 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
304 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
305 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
306 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
307 <conditional name="cond_filter"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
308 <param name="select_filter" value="yes" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
309 <conditional name="cond_region"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
310 <param name="select_region" value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
311 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
312 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
313 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
314 </test> |
|
3
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
315 <!-- count alignments --> |
|
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
316 <test> |
|
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
317 <param name="input" value="test.bam" ftype="bam" /> |
|
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
318 <param name="outtype" value="count" /> |
|
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
319 <output name="outputcnt" file="test_counts.tab" ftype="txt" /> |
|
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
320 </test> |
|
0
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
321 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
322 <param name="input" value="test.sam" ftype="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
323 <param name="outtype" value="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
324 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
325 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
326 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
327 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
328 <conditional name="cond_filter"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
329 <param name="select_filter" value="yes" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
330 <conditional name="cond_region"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
331 <param name="select_region" value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
332 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
333 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
334 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
335 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
336 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
337 <param name="input" value="test.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
338 <param name="outtype" value="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
339 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
340 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
341 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
342 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
343 <conditional name="cond_filter"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
344 <param name="select_filter" value="yes" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
345 <conditional name="cond_region"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
346 <param name="select_region" value="text"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
347 <param name="regions" value="CHROMOSOME_I" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
348 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
349 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
350 <output name="outputsam" file="test.cram" ftype="cram" compare="sim_size" delta="250" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
351 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
352 <!-- bam to sam + header options (adapted from bam_to_sam tool)--> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
353 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
354 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
355 <param name="outtype" value="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
356 <param name="header" value="-h" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
357 <output file="bam_to_sam_out1.sam" ftype="sam" name="outputsam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
358 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
359 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
360 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
361 <param name="outtype" value="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
362 <param name="header" value="-H" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
363 <output file="bam_to_sam_out2.sam" ftype="sam" name="outputsam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
364 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
365 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
366 <param ftype="bam" name="input" value="bam_to_sam_in1.bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
367 <param name="outtype" value="sam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
368 <param name="header" value="" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
369 <output file="bam_to_sam_out3.sam" ftype="sam" name="outputsam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
370 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
371 <!-- cram to bam + region (adapted from cram_to_bam tool)--> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
372 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
373 <param name="input" value="test.cram" ftype="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
374 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
375 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
376 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
377 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
378 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
379 <output name="outputsam" file="test.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
380 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
381 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
382 <param name="input" value="test.cram" ftype="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
383 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
384 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
385 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
386 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
387 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
388 <param name="target_region" value="region" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
389 <param name="region_string" value="CHROMOSOME_I" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
390 <output name="outputsam" file="test.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
391 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
392 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
393 <param name="input" value="test.cram" ftype="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
394 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
395 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
396 <param name="addref_select" value="history" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
397 <param name="ref" value="test.fa" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
398 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
399 <param name="target_region" value="regions_bed_file" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
400 <param name="regions_bed_file" value="test.bed" ftype="bed" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
401 |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
402 <output name="outputsam" file="test.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
403 </test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
404 <test> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
405 <param name="input" value="test2.cram" dbkey="equCab2" ftype="cram" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
406 <param name="outtype" value="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
407 <conditional name="addref_cond"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
408 <param name="addref_select" value="cached" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
409 <param name="ref" value="equCab2chrM" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
410 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
411 <conditional name="cond_region"> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
412 <param name="select_region" value="no"/> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
413 </conditional> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
414 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" /> |
|
5b44ef788111
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
415 </test> |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
416 <!-- sampling options--> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
417 <test> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
418 <param name="input" value="test.sam" ftype="sam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
419 <param name="outtype" value="sam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
420 <conditional name="cond_subsample"> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
421 <param name="select_subsample" value="target" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
422 <param name="target" value="2" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
423 </conditional> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
424 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
425 </test> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
426 <test> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
427 <param name="input" value="test.sam" ftype="sam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
428 <param name="outtype" value="sam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
429 <conditional name="cond_subsample"> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
430 <param name="select_subsample" value="target" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
431 <param name="seed" value="7" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
432 <param name="target" value="2" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
433 </conditional> |
|
3
097c44aaf6d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
434 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" /> |
|
2
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
435 </test> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
436 <test> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
437 <param name="input" value="test.bam" ftype="bam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
438 <param name="outtype" value="bam" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
439 <conditional name="cond_subsample"> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
440 <param name="select_subsample" value="target" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
441 <param name="seed" value="7" /> |
|
80d8ca44f8da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
442 <param name="target" value="2" /> |
|
80d8ca44f8da
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443 </conditional> |
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444 <output name="outputsam" file="test_ds.bam" ftype="bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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445 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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446 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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447 <param name="input" value="test.bam" ftype="bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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448 <param name="outtype" value="bam" /> |
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449 <conditional name="cond_subsample"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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450 <param name="select_subsample" value="fraction" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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451 <param name="seed" value="7" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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452 <param name="fraction" value=".2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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453 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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454 <output name="outputsam" file="test_ds.bam" ftype="bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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455 </test> |
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0
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456 </tests> |
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457 <help> |
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458 **What it does** |
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459 |
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460 Samtools view can: |
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461 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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462 1. filter alignments according to various criteria |
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463 2. convert between alignment formats (SAM, BAM, CRAM) |
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464 |
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465 With no options or regions specified, prints all alignments in the specified input alignment file (in SAM, BAM, or CRAM format) to standard output in SAM format (with no header). |
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466 |
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467 **Alignment format conversion** |
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468 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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469 Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type". |
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470 |
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471 .. class:: infomark |
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472 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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473 samtools view allows to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of reference sequence in the CRAM format is detailed. |
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474 CRAM is (intended as a primarily) a reference-based compressed format, i.e. only differences between the stored sequences and the reference are stored. As a consequence the reference that was used to generate the alignemnts is always needed in order to interpret the alignments (a checksum stored in the CRAM file is used to verify that the only the correct sequence can be used), i.e. the CRAM file on its own is not useful per default. This allows for a more space efficient storage compared to BAM. |
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475 But it is also possible to use CRAM without a reference with the disadvantage that the reference is stored explicitely (as in SAM and BAM). |
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476 |
|
1
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477 The Galaxy tool **currently generates only CRAM without reference sequence**. |
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478 |
|
1
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479 For reference based CRAM input the correct refernce sequence needs to be specified. |
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480 |
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481 **Filtering alignments** |
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482 |
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483 samtools view allows to filter alignements based on various criteria, i.e. the output will contain only alignemnts matching all criteria (an additional output containing the remaining alignments can be created additionally, see "Output alignments not passing the filter" in "output options"): e.g. by regions (see below), alignment quality (see below), and tags or flags set in the alignments. |
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484 |
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485 |
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486 |
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487 **Filtering by regions** |
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488 |
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489 You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format). |
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490 |
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491 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. |
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492 |
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493 Important note: when multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions. |
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494 |
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495 Examples of region specifications: |
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496 |
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497 - chr1 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1). |
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498 - chr2:1000000 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome. |
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499 - chr3:1000-2000 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions). |
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500 - '*' Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.) |
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501 - . Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.) |
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502 |
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503 **Filtering by quality** |
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504 |
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505 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignemnt. Note that aligners do not follow a consistent definition. |
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506 |
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507 The -x, -B, and -s options modify the data which is contained in each alignment. |
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508 </help> |
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509 <expand macro="citations"/> |
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510 </tool> |