Mercurial > repos > iuc > samtools_view
annotate samtools_view.xml @ 16:2dce91e11ca7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
| author | iuc |
|---|---|
| date | Fri, 30 Aug 2024 10:24:46 +0000 |
| parents | 6be888be75f9 |
| children | 32dc5f781059 |
| rev | line source |
|---|---|
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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changeset
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> |
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0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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3 <macros> |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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4 <import>macros.xml</import> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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5 <token name="@REF_DATA@"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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6 ## additional reference data |
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c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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7 #if $use_ref: |
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c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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8 -T "\$reffa" |
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c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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9 -t "\$reffai" |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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10 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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11 </token> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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12 <xml name="read_output_formatting"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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13 <yield /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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14 <section name="adv_output" title="Read Reformatting Options" expanded="false"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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15 <repeat name="readtags" title="Strip read tags from output"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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16 <param name="readtag" type="text" argument="-x" label="Read tag to strip" help="Read tag to exclude from output."/> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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17 </repeat> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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18 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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19 </section> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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20 </xml> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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21 <xml name="output_format_selector"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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22 <conditional name="output_format"> |
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8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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23 <param name="oformat" type="select" label="Output format" |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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24 help="Note on BAM output format: The tool will generate coordinate-sorted BAM, i.e., may change the order of reads compared to the input. For BAM input, select 'Same as input' to produce BAM output with the read order retained."> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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25 <option value="input">Same as input</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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26 <option value="sam">SAM</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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27 <option value="bam" selected="True">BAM (-b)</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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28 <option value="cram">CRAM (-C)</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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29 </param> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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30 <when value="input" /> |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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31 <when value="sam"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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32 <yield /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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33 </when> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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34 <when value="bam" /> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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35 <when value="cram" /> |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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36 </conditional> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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37 </xml> |
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0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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38 </macros> |
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2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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39 <expand macro="requirements"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1354b1358df89a922c3243f7e27ce789094b8644"
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40 <requirement type="package" version="5.1.0">gawk</requirement> |
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02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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41 </expand> |
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0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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42 <expand macro="stdio"/> |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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43 <expand macro="version_command"/> |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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44 <command><![CDATA[ |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 @ADDTHREADS@ |
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9
b72793637686
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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46 @ADDMEMORY@ |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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47 ## prepare reference data |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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48 @PREPARE_FASTA_IDX@ |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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49 @PREPARE_IDX@ |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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50 |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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51 ## determine the output format flag to pass to samtools view |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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52 ## -c for count mode |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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53 ## -b to produce BAM-formatted output |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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54 ## -C to produce CRAM-formatted output |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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55 ## SAM is the default ouput format |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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56 #set $fmtopt = '' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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57 #if str($mode.output_options.reads_report_type) == 'count': |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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58 #set $fmtopt = '-c' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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59 #else: |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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60 #if str($mode.output_options.output_format.oformat) == 'bam': |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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61 #set $fmtopt = '-b' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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62 #elif str($mode.output_options.output_format.oformat) == 'cram': |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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63 #set $fmtopt = '-C' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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64 #elif str($mode.output_options.output_format.oformat) == 'input': |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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65 #if $input.is_of_type('bam'): |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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66 #set $fmtopt = '-b' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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67 #elif $input.is_of_type('cram'): |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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68 #set $fmtopt = '-C' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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69 #else: |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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70 ## input in SAM format, make sure to keep header if present |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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71 #set $fmtopt = '-h' |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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72 #end if |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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|
73 #end if |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
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diff
changeset
|
74 #end if |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
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|
75 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
76 #if str($mode.outtype) == 'header': |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
77 ## call samtools view and be done |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
78 samtools view |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
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|
79 -H $fmtopt -o outfile |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
80 @REF_DATA@ |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
81 infile |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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82 #else: |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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83 ## are filtering and/or subsampling in effect? |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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84 #set $with_filtering = False |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
85 #set $with_subsampling = False |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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86 #if str($mode.outtype) == 'selected_reads': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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87 #set $with_filtering = True |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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88 #if str($mode.subsample_config.subsampling_mode.select_subsample) != 'fraction' or $mode.subsample_config.subsampling_mode.factor > 1: |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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89 #set $with_subsampling = True |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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90 #end if |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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91 #end if |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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92 |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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93 ## are we producing one or two outputs? |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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94 #if str($mode.outtype) == 'selected_reads' and str($mode.output_options.reads_report_type) != 'count' and str($mode.output_options.complementary_output) == 'yes': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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95 #set $with_non_selected_reads_output = True |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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96 #else: |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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97 #set $with_non_selected_reads_output = False |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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98 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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99 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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100 #set $std_filters = '' |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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101 #set $reg_filters = '' |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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102 #if $with_filtering: |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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103 ## build string of all user-configured filter options |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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104 #if str($mode.filter_config.cond_region.select_region) == 'bed': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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105 #set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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106 #elif str($mode.filter_config.cond_region.select_region) == 'text': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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107 #set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip() |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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108 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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109 |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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110 #if $mode.filter_config.cond_rg.select_rg == 'text': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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111 #set $std_filters = $std_filters + " -r '%s'" % str($mode.filter_config.cond_rg.readgr) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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112 #else if $mode.filter_config.cond_rg.select_rg == 'file': |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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113 #set $std_filters = $std_filters + " -R '%s'" % str($mode.filter_config.cond_rg.rgfile) |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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114 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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115 #if str($mode.filter_config.quality) != '' and int($mode.filter_config.quality) > 0: |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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116 #set $std_filters = $std_filters + " -q %s" % str($mode.filter_config.quality) |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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117 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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118 #if str($mode.filter_config.library): |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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119 #set $std_filters = $std_filters + " -l '%s'" % str($mode.filter_config.library) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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120 #end if |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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121 #if str($mode.filter_config.cigarcons): |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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122 #set $std_filters = $std_filters + " -m %s" % str($mode.filter_config.cigarcons) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
123 #end if |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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124 #set $filter = $mode.filter_config.inclusive_filter |
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350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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125 @FLAGS@ |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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126 #set $std_filters = $std_filters + " -f %s" % str($flags) |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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127 #set $filter = $mode.filter_config.exclusive_filter |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
128 @FLAGS@ |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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129 #set $std_filters = $std_filters + " -F %s" % str($flags) |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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130 #set $filter = $mode.filter_config.exclusive_filter_all |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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131 @FLAGS@ |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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132 #set $std_filters = $std_filters + " -G %s" % str($flags) |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
133 #if $mode.filter_config.tag: |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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134 #set $std_filters = $std_filters + " --tag '%s'" % $mode.filter_config.tag |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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diff
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|
135 #end if |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
136 #if $mode.filter_config.qname_file: |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
137 #set std_filters = $std_filters + " --qname-file '%s'" % $mode.filter_config.qname_file |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
138 #end if |
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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diff
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|
139 #if str($cond_expr.select_expr) == "yes": |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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|
140 #set std_filters = $std_filters + " -e '%s'" % $cond_expr.expression |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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diff
changeset
|
141 #end if |
|
0
00d1f08bdcdc
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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|
142 #end if |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
143 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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diff
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144 #if $with_subsampling: |
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145 ## handle seed and fraction calculation for subsampling |
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146 #import random |
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147 #if str($mode.subsample_config.subsampling_mode.seed): |
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148 #set $seed = int($mode.subsample_config.subsampling_mode.seed) |
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149 #else: |
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150 #set $seed = random.randrange(32768) |
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151 #end if |
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152 |
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153 #if $mode.subsample_config.subsampling_mode.select_subsample == 'target': |
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154 ##this must be done before the main command because we don't know the total # reads until execution time |
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155 #if $input.is_of_type('sam') or $std_filters or $reg_filters: |
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156 ## There is no index or we cannot use it because we are |
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157 ## not dealing with all of the reads in the indexed |
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158 ## file. We have to do an extra pass over the input to |
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159 ## count the reads to subsample. |
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160 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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161 #else: |
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162 ## We can get the count of reads to subsample using |
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163 ## an inexpensive call to idxstats. |
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164 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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165 #end if |
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166 #end if |
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167 #end if |
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168 |
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169 ## call samtools view |
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170 samtools view |
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171 -@ \$addthreads |
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172 $fmtopt |
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173 |
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174 ## filter options (except regions filter, which is the last parameter) |
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175 $std_filters |
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176 #if $with_subsampling: |
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177 --subsample-seed $seed |
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178 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target": |
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179 ##this is calculated at execution time before the main samtools command |
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180 --subsample \${sample_fragment} |
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181 #else: |
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182 #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor) |
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183 --subsample $fraction |
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184 #end if |
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185 #end if |
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186 |
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187 ## output options |
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188 #if str($mode.output_options.reads_report_type) == 'count': |
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189 -o outfile |
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190 #else: |
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191 ## output options |
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192 #if str($mode.output_options.output_format.oformat) == 'sam': |
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193 ${mode.output_options.output_format.with_header} |
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194 #end if |
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195 ${mode.output_options.adv_output.collapsecigar} |
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196 #for $s in $mode.output_options.adv_output.readtags: |
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197 -x '${s.readtag}' |
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198 #end for |
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199 #if str($mode.output_options.reads_report_type) == 'retained' |
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200 -o outfile |
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201 #if $with_non_selected_reads_output: |
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202 -U inv_outfile |
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203 #end if |
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204 #else: |
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205 -U outfile |
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206 #if $with_non_selected_reads_output: |
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207 -o inv_outfile |
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208 #else: |
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209 -o /dev/null |
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210 #end if |
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211 #end if |
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0
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212 |
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213 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963) |
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214 #if $mode.output_options.output_format.oformat == 'cram': |
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215 --output-fmt-option no_ref |
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216 #end if |
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0
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217 #end if |
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218 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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219 @REF_DATA@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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220 |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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221 infile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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222 |
|
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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223 ## region filter needs to be at the end |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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224 $reg_filters |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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225 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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226 #if str($mode.output_options.reads_report_type) != 'count': |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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227 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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228 ## then sort the output by coordinate, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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229 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam': |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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230 && samtools sort |
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9
b72793637686
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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231 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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232 -O bam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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233 -o tmpsam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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234 outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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235 && mv tmpsam outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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236 #if $with_non_selected_reads_output: |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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237 && samtools sort |
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9
b72793637686
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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238 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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239 -O bam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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240 -o tmpsam |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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241 inv_outfile |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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242 && mv tmpsam inv_outfile |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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243 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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244 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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245 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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246 |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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247 ##end of reads and count-specific section |
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0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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248 #end if |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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249 ]]></command> |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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250 <inputs> |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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251 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) --> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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252 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" /> |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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253 <conditional name="mode"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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254 <param name="outtype" type="select" label="What would you like to look at?"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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255 <option value="all_reads">All reads in the input dataset</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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256 <option value="selected_reads">A filtered/subsampled selection of reads</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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257 <option value="header">Just the input header (-H)</option> |
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0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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258 </param> |
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7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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259 <when value="all_reads"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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260 <conditional name="output_options"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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261 <param name="reads_report_type" type="select" label="What would you like to have reported?"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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262 <option value="retained">The actual reads</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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263 <option value="count">The count of reads (-c)</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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264 </param> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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265 <when value="retained"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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266 <expand macro="read_output_formatting" /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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267 <expand macro="output_format_selector"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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268 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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269 label="Include SAM header in the output?" /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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270 </expand> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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271 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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272 <when value="count" /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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273 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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274 </when> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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275 <when value="selected_reads"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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276 <section name="filter_config" title="Configure filters" expanded="false"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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277 <conditional name="cond_region"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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278 <param name="select_region" type="select" label="Filter by regions"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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279 <option value="no" selected="True">No</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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280 <option value="text">Manualy specify regions</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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281 <option value="bed">Regions from BED file</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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282 </param> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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283 <when value="no"/> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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284 <when value="text"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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285 <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)."/> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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286 </when> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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287 <when value="bed"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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288 <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." /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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289 </when> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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290 </conditional> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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291 <conditional name="cond_rg"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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292 <param name="select_rg" type="select" label="Filter by readgroup"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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293 <option value="no" selected="True">No</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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294 <option value="text">Single read group </option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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295 <option value="file">Read groups from file</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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296 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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297 <when value="no"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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298 <when value="text"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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299 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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300 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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301 <when value="file"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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302 <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." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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303 </when> |
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304 </conditional> |
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16
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305 <conditional name="cond_expr"> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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306 <param name="select_expr" type="select" label="Filter by expression"> |
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307 <option value="no" selected="True">No</option> |
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308 <option value="yes">Filter using an expression (see manual)</option> |
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309 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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310 <when value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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311 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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312 <param name="expression" type="text" argument="-e" label="Filter by expression - for example sclen>0 will filter all soft clipped reads" help="See Samtools manual for Filter expression syntax"> |
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313 <sanitizer invalid_char=""> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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314 <valid initial="string.printable"> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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315 <remove value=" "/> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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316 <remove value="'"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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317 <remove value='"'/> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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318 </valid> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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319 </sanitizer> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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320 </param> |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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321 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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322 </conditional> |
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7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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323 <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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324 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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325 <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." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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326 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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327 <expand macro="flag_options" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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328 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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329 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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330 <expand macro="flag_options" /> |
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0
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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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331 </param> |
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7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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332 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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333 <expand macro="flag_options" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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334 </param> |
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10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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335 <param argument="--tag" type="text" optional="true" label="Filter by tag" help="Only include reads with tag STR1 and associated value STR2. Write in the format STR1:STR2 (see help for more details)." /> |
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350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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336 <!-- TODO implement -D --> |
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11
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1d2666cfe206ef538fd811dbccaec2e8f3c6f7f0"
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337 <param argument="--qname-file" format="txt" optional="true" type="data" label="Filter by readnames" help="Only output alignments with readnames that are listed in this file." /> |
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7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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338 </section> |
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339 <section name="subsample_config" title="Configure subsampling" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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340 <conditional name="subsampling_mode"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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341 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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342 <option value="fraction">Specify a downsampling factor</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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343 <option value="target">Specify a target # of reads</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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344 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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345 <when value="fraction"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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346 <param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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347 <expand macro="seed_input" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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348 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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349 <when value="target"> |
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8
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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350 <param name="target" type="integer" optional="False" min="1" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." /> |
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7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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351 <expand macro="seed_input" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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352 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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353 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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354 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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355 <conditional name="output_options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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356 <param name="reads_report_type" type="select" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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357 label="What would you like to have reported?" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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358 help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'."> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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359 <option value="retained">All reads retained after filtering and subsampling</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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360 <option value="dropped">Reads dropped during filtering and subsampling</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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361 <option value="count">The count of retained reads (-c)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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362 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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363 <when value="retained"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
364 <expand macro="read_output_formatting"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
365 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false" |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
366 label="Produce extra dataset with dropped reads?" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
367 </expand> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
368 <expand macro="output_format_selector"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
369 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
370 label="Include SAM header in the output?" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
371 </expand> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
372 </when> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
373 <when value="dropped"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
374 <expand macro="read_output_formatting"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
375 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false" |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
376 label="Produce extra dataset with retained reads?" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
377 </expand> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
378 <expand macro="output_format_selector"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
379 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
380 label="Include SAM header in the output?" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
381 </expand> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
382 </when> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
383 <when value="count" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
384 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
385 </when> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
386 <when value="header"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
387 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
388 <param name="reads_report_type" type="select" label="What would you like to have reported?"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
389 <option value="">The header in ...</option> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
390 </param> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
391 <when value=""> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
392 <expand macro="output_format_selector" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
393 </when> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
394 </conditional> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
395 </when> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
396 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
397 <expand macro="optional_reference" argument="-t" help="Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help)."/> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
398 </inputs> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
399 <outputs> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
400 <!-- TODO do I need an action for dbkey? --> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
401 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments"> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
402 <filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
403 <change_format> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
404 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
405 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
406 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
407 </change_format> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
408 </data> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
409 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments"> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
410 <filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
411 <change_format> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
412 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
413 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
414 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
415 </change_format> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
416 </data> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
417 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
418 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
419 </data> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
420 </outputs> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
421 <tests> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
422 <!-- 1) sam to bam (copied from the sam_to_bam tool) --> |
|
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
423 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
424 <param name="input" ftype="sam" value="in_test_1.sam" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
425 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
426 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
427 <!-- 2) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
428 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
429 <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
430 <conditional name="addref_cond"> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
431 <param name="addref_select" value="cached" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
432 <param name="ref" value="equCab2chrM" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
433 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
434 <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
435 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
436 <!-- 3) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
437 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
438 <param name="input" ftype="sam" value="in_test_3.sam" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
439 <conditional name="addref_cond"> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
440 <param name="addref_select" value="history" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
441 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
442 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
443 <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
444 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
445 <!-- 4) cram to bam --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
446 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
447 <param name="input" value="in_test_4.cram" ftype="cram" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
448 <conditional name="addref_cond"> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
449 <param name="addref_select" value="history" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
450 <param name="ref" value="test.fa" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
451 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
452 <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
453 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
454 <!-- 5) within bam operations expected to result in sorting or not --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
455 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
456 <!-- sorted bam should always result in unmodifed output --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
457 <param name="input" ftype="bam" value="in_test_5.bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
458 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
459 <not_has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
460 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
461 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
|
4
fdc58a0cc1d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
462 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
463 <!-- 6) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
464 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
465 <!-- sorted bam should always result in unmodifed output --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
466 <param name="input" ftype="bam" value="in_test_5.bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
467 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
468 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
469 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
470 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
471 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
472 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
473 </conditional> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
474 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
475 <not_has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
476 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
477 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
478 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
479 <!-- 7) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
480 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
481 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
482 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
483 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
484 <has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
485 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
486 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
487 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
488 <!-- 8) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
489 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
490 <!-- ... but should be emitted unmodifed when using input format --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
491 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
492 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
493 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
494 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
495 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
496 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
497 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
498 </conditional> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
499 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
500 <not_has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
501 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
502 <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
503 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
504 <!-- 9) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
505 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
506 <!-- unsorted.bam should get sorted during "conversion" to bam ... --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
507 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
508 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
509 <has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
510 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
511 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
512 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
513 <!-- 10) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
514 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
515 <!-- ... ... but should be emitted unmodifed when using input format --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
516 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
517 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
518 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
519 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
520 <param name="oformat" value="input" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
521 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
522 </conditional> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
523 </conditional> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
524 <assert_command> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
525 <not_has_text text="samtools sort" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
526 </assert_command> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
527 <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
528 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
529 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)--> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
530 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
531 <param ftype="bam" name="input" value="in_test_11.bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
532 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
533 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
534 <conditional name="output_format"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
535 <param name="oformat" value="sam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
536 <param name="with_header" value="true" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
537 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
538 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
539 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
540 <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
541 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
542 <!-- 12) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
543 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
544 <param ftype="bam" name="input" value="in_test_11.bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
545 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
546 <param name="outtype" value="header" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
547 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
548 <conditional name="output_format"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
549 <param name="oformat" value="sam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
550 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
551 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
552 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
553 <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
554 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
555 <!-- 13) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
556 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
557 <param ftype="bam" name="input" value="in_test_11.bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
558 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
559 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
560 <conditional name="output_format"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
561 <param name="oformat" value="sam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
562 <param name="with_header" value="false" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
563 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
564 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
565 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
566 <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
567 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
568 <!-- 14) count alignments --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
569 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
570 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
571 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
572 <param name="outtype" value="all_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
573 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
574 <param name="reads_report_type" value="count" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
575 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
576 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
577 <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
578 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
579 <!-- 15) region filters --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
580 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
581 <param name="input" value="in_test_15.sam" ftype="sam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
582 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
583 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
584 <section name="filter_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
585 <conditional name="cond_region"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
586 <param name="select_region" value="no"/> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
587 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
588 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
589 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
590 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
591 <param name="oformat" value="cram" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
592 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
593 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
594 </conditional> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
595 <conditional name="addref_cond"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
596 <param name="addref_select" value="history" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
597 <param name="ref" value="test.fa" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
598 </conditional> |
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
599 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="500" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
600 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
601 <!-- 16) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
602 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
603 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
604 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
605 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
606 <section name="filter_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
607 <conditional name="cond_region"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
608 <param name="select_region" value="no"/> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
609 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
610 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
611 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
612 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
613 <param name="oformat" value="cram" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
614 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
615 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
616 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
617 <conditional name="addref_cond"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
618 <param name="addref_select" value="history" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
619 <param name="ref" value="test.fa" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
620 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
621 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
622 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
623 <!-- 17) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
624 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
625 <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
626 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
627 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
628 <section name="filter_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
629 <conditional name="cond_region"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
630 <param name="select_region" value="no"/> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
631 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
632 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
633 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
634 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
635 <param name="oformat" value="bam" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
636 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
637 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
638 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
639 <conditional name="addref_cond"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
640 <param name="addref_select" value="cached" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
641 <param name="ref" value="equCab2chrM" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
642 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
643 <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
644 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
645 <!-- 18) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
646 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
647 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
648 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
649 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
650 <section name="filter_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
651 <conditional name="cond_region"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
652 <param name="select_region" value="text"/> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
653 <param name="regions" value="CHROMOSOME_I" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
654 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
655 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
656 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
657 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
658 <param name="oformat" value="cram" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
659 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
660 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
661 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
662 <conditional name="addref_cond"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
663 <param name="addref_select" value="history" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
664 <param name="ref" value="test.fa" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
665 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
666 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
667 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
668 <!-- 19) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
669 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
670 <param name="input" value="test_15.cram" ftype="cram" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
671 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
672 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
673 <section name="filter_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
674 <conditional name="cond_region"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
675 <param name="select_region" value="text"/> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
676 <param name="regions" value="CHROMOSOME_I" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
677 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
678 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
679 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
680 <conditional name="output_format"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
681 <param name="oformat" value="bam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
682 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
683 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
684 </conditional> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
685 <conditional name="addref_cond"> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
686 <param name="addref_select" value="history" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
687 <param name="ref" value="test.fa" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
688 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
689 <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
690 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
691 <!-- 20) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
692 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
693 <param name="input" value="test_15.cram" ftype="cram" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
694 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
695 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
696 <section name="filter_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
697 <conditional name="cond_region"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
698 <param name="select_region" value="bed" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
699 <param name="bedfile" value="test.bed" ftype="bed" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
700 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
701 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
702 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
703 <conditional name="output_format"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
704 <param name="oformat" value="bam" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
705 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
706 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
707 </conditional> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
708 <conditional name="addref_cond"> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
709 <param name="addref_select" value="history" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
710 <param name="ref" value="test.fa" /> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
711 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
712 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
713 </test> |
|
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
714 <!-- 21) sampling options target < total reads --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
715 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
716 <param name="input" value="in_test_15.sam" ftype="sam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
717 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
718 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
719 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
720 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
721 <param name="select_subsample" value="target" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
722 <param name="target" value="2" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
723 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
724 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
725 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
726 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
727 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
728 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
729 </conditional> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
730 </conditional> |
|
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
731 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
732 </test> |
|
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
733 <!-- 22) target > total reads --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
734 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
735 <param name="input" value="in_test_15.sam" ftype="sam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
736 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
737 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
738 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
739 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
740 <param name="select_subsample" value="target" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
741 <param name="target" value="20" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
742 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
743 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
744 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
745 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
746 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
747 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
748 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
749 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
750 <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
751 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
752 <!-- 23) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
753 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
754 <!-- subsampling SAM input without reads --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
755 <param name="input" value="in_test_23.sam" ftype="sam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
756 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
757 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
758 <section name="subsample_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
759 <conditional name="subsampling_mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
760 <param name="select_subsample" value="target" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
761 <param name="target" value="20" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
762 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
763 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
764 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
765 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
766 <param name="oformat" value="input" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
767 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
768 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
769 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
770 <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
771 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
772 <!-- 24) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
773 <test expect_num_outputs="1"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
774 <!-- subsampling BAM input without reads --> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
775 <param name="input" value="in_test_24.bam" ftype="bam" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
776 <conditional name="mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
777 <param name="outtype" value="selected_reads" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
778 <section name="subsample_config"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
779 <conditional name="subsampling_mode"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
780 <param name="select_subsample" value="target" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
781 <param name="target" value="20" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
782 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
783 </section> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
784 <conditional name="output_options"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
785 <conditional name="output_format"> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
786 <param name="oformat" value="input" /> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
787 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
788 </conditional> |
|
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
789 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
790 <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" /> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
791 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
792 <!-- 25) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
793 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
794 <param name="input" value="in_test_15.sam" ftype="sam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
795 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
796 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
797 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
798 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
799 <param name="select_subsample" value="target" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
800 <param name="seed" value="7" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
801 <param name="target" value="2" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
802 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
803 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
804 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
805 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
806 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
807 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
808 </conditional> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
809 </conditional> |
|
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
810 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
811 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
812 <!-- 26) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
813 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
814 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
815 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
816 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
817 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
818 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
819 <param name="select_subsample" value="target" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
820 <param name="seed" value="7" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
821 <param name="target" value="2" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
822 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
823 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
824 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
825 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
826 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
827 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
828 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
829 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
830 <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
831 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
832 <!-- 27) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
833 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
834 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
835 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
836 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
837 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
838 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
839 <param name="select_subsample" value="target" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
840 <param name="seed" value="7" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
841 <param name="target" value="20" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
842 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
843 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
844 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
845 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
846 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
847 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
848 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
849 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
850 <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
851 </test> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
852 <!-- 28) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
853 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
854 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
855 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
856 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
857 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
858 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
859 <param name="select_subsample" value="fraction" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
860 <param name="seed" value="7" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
861 <param name="factor" value="5" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
862 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
863 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
864 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
865 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
866 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
867 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
868 </conditional> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
869 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
870 <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
871 </test> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
872 <!-- 29) --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
873 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
874 <param name="input" value="in_test_14.bam" ftype="bam" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
875 <conditional name="mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
876 <param name="outtype" value="selected_reads" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
877 <section name="subsample_config"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
878 <conditional name="subsampling_mode"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
879 <param name="select_subsample" value="fraction" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
880 <param name="seed" value="7" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
881 <param name="factor" value="1.25" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
882 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
883 </section> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
884 <conditional name="output_options"> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
885 <param name="reads_report_type" value="dropped" /> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
886 <conditional name="output_format"> |
|
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
887 <param name="oformat" value="input" /> |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
888 </conditional> |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
889 </conditional> |
|
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
890 </conditional> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
891 <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
892 </test> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
893 <!-- 30) testing tag filtering --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
894 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
895 <param name="input" value="in_test_30.bam" ftype="bam" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
896 <conditional name="mode"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
897 <param name="outtype" value="selected_reads" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
898 <section name="filter_config"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
899 <param name="tag" value="XS:-18" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
900 </section> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
901 <conditional name="output_options"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
902 <conditional name="output_format"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
903 <param name="oformat" value="bam" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
904 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
905 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
906 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
907 <assert_command> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
908 <has_text text="--tag 'XS:-18'"/> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
909 </assert_command> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
910 <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
911 </test> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
912 <!-- 31) testing readname filtering --> |
|
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
913 <test expect_num_outputs="1"> |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
914 <param name="input" value="in_test_30.bam" ftype="bam" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
915 <conditional name="mode"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
916 <param name="outtype" value="selected_reads" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
917 <section name="filter_config"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
918 <param name="qname_file" value="readnames.txt" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
919 </section> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
920 <conditional name="output_options"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
921 <conditional name="output_format"> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
922 <param name="oformat" value="bam" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
923 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
924 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
925 </conditional> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
926 <assert_command> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
927 <has_text text="--qname-file"/> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
928 </assert_command> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
929 <output name="outputsam" file="test_31.bam" ftype="bam" lines_diff="2" /> |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
930 </test> |
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
931 <!-- 32) testing expression filters --> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
932 <test expect_num_outputs="1"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
933 <param name="input" value="in_test_30.bam" ftype="bam"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
934 <conditional name="mode"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
935 <param name="outtype" value="selected_reads" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
936 <section name="filter_config"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
937 <conditional name="cond_expr"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
938 <param name="select_expr" value="yes"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
939 <param name="expression" value="sclen>0"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
940 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
941 </section> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
942 <conditional name="output_options"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
943 <conditional name="output_format"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
944 <param name="oformat" value="bam" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
945 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
946 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
947 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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15
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|
948 <assert_command> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
949 <has_text text="-e 'sclen>0'"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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15
diff
changeset
|
950 </assert_command> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
951 <output name="outputsam" file="test_32.bam" ftype="bam" lines_diff="2" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
952 </test> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
953 <!-- 33) testing expression filters --> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
954 <test expect_num_outputs="1"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
955 <param name="input" value="in_test_30.bam" ftype="bam"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
956 <conditional name="mode"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
957 <param name="outtype" value="selected_reads" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
958 <section name="filter_config"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
959 <conditional name="cond_expr"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
960 <param name="select_expr" value="yes"/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
961 <param name="expression" value='rname!="chr13"'/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
962 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
963 </section> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
964 <conditional name="output_options"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
965 <conditional name="output_format"> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
966 <param name="oformat" value="bam" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
967 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
968 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
969 </conditional> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
970 <assert_command> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
971 <has_text text="-e 'rname!="/> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
972 </assert_command> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
973 <output name="outputsam" file="test_33.bam" ftype="bam" lines_diff="2" /> |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
974 </test> |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
975 </tests> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
976 <help> |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
977 **What it does** |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
978 |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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|
979 Samtools view can: |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
980 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
981 1. convert between alignment formats (SAM, BAM, CRAM) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
982 2. filter and subsample alignments according to user-specified criteria |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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983 3. count the reads in the input dataset or those retained after filtering |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
984 and subsampling |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
985 4. obtain just the header of the input in any supported format |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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|
986 |
|
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
987 In addition, the tool has (limited) options to modify read records during conversion and/or filtering by: |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
988 |
|
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
989 - stripping them of user-specified tags |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
990 - collapsing backward CIGAR operations if they are specified in their CIGAR |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
991 fields |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
992 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
993 With default settings, the tool generates a BAM dataset with the header and |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
994 reads found in the input dataset (which can be in SAM, BAM, or CRAM format). |
|
0
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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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|
995 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
996 **Alignment format conversion** |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
997 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
998 By changing the *Output format* it is possible to convert an input dataset to |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
999 another format. |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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|
1000 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". |
|
0
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|
1001 |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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|
1002 .. class:: infomark |
|
0
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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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|
1003 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1004 The tool allows you 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 the reference sequence in the CRAM format is detailed. |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1005 CRAM is (primarily) a reference-based compressed format, i.e. only sequence differences between aligned reads and the reference are stored. As a consequence, the reference that was used during read mapping is needed in order to interpret the alignment records (a checksum stored in the CRAM file is used to verify that only the correct reference sequence can be used). This allows for more space-efficient storage than with BAM format, but such a CRAM file is not usable without its reference. |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1006 It is also possible, however, to use CRAM without a reference with the disadvantage that the reference sequence gets stored then explicitely (as in SAM and BAM). |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
1007 |
|
1
6ade12d94f9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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0
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|
1008 The Galaxy tool **currently generates only CRAM without reference sequence**. |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
1009 |
|
1
6ade12d94f9a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c7bb87a32997810fd9f28572fc5af628c8c4ffa3
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0
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changeset
|
1010 For reference based CRAM input the correct refernce sequence needs to be specified. |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
1011 |
|
00d1f08bdcdc
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
|
1012 **Filtering alignments** |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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|
1013 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1014 If you ask for *A filtered/subsampled selection of reads*, the tool will allow |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
1015 you to specify filter conditions and/or to choose a subsampling strategy, and |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1016 the output will contain one of the following depending on your choice under |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1017 *What would you like to have reported?*: |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1018 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1019 - All reads retained after filtering and subsampling |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1020 - Reads dropped during filtering and subsampling |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1021 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1022 If instead you want to *split* the input reads based on your criteria and |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1023 obtain *two* datasets, one with the retained and one with the dropped reads, check |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1024 the *Produce extra dataset with dropped/retained reads?* option. |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1025 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1026 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1027 **Filtering by regions** |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1028 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1029 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). |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1030 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1031 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1032 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1033 .. class:: Warning mark |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1034 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1035 When multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions. |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1036 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1037 Examples of region specifications: |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1038 |
|
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1039 ``chr1`` |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1040 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1). |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1041 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1042 ``chr2:1000000`` |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1043 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome. |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1044 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1045 ``chr3:1000-2000`` |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1046 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions). |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1047 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1048 ``*`` |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1049 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.) |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1050 |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1051 ``.`` |
|
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1052 Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.) |
|
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1053 |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1054 **Filtering by quality** |
|
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
1055 |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1056 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignment. Note that aligners do not follow a consistent definition. |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1057 |
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1058 **Filtering by Tag** |
|
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1059 |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1060 This filter allows to select reads based on tool or user specific tags, e.g., XS:i:-18 the alignment score tag of bowtie. |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1061 Thus to filter for a specific value of the tag you need the format STR1:STR2, e.g., XS:-18 to filter reads with an aligment score of -18. |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1062 You can also just write STR1 without the value STR2 hence the filter selects all reads with the tag STR1, e.g., XS. |
|
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1063 |
|
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1064 **Filtering by Expression** |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1065 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1066 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1067 Filter expressions are used as an on-the-fly checking of incoming SAM, BAM or CRAM records, discarding records that do not match the specified expression. |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1068 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1069 The language used is primarily C style, but with a few differences in the precedence rules for bit operators and the inclusion of regular expression |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1070 matching. |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1071 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1072 The operator precedence, from strongest binding to weakest, is |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1073 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1074 :: |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1075 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1076 Grouping (, ) E.g. "(1+2)*3" |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1077 Values: literals, vars Numbers, strings and variables |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1078 Unary ops: +, -, !, ~ E.g. -10 +10, !10 (not), ~5 (bit not) |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1079 Math ops: \*, /, % Multiply, division and (integer) modulo |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1080 Math ops: +, - Addition / subtraction |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1081 Bit-wise: & Integer AND |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1082 Bit-wise ^ Integer XOR |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1083 Bit-wise | Integer OR |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1084 Conditionals: >, >=, <, <= |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1085 Equality: \=\=, !=, =~, !~ =~ and !~ match regular expressions |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1086 Boolean: &&, || Logical AND / OR |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1087 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1088 |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1089 Expressions are computed using floating point mathematics, so "10 / 4" evaluates to 2.5 rather than 2. They may be written as integers in decimal or |
|
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
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|
1090 "0x" plus hexadecimal, and floating point with or without exponents.However operations that require integers first do an implicit type conversion, so |
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1091 "7.9 % 5" is 2 and "7.9 & 4.1" is equivalent to "7 & 4", which is 4. Strings are always specified using double quotes. To get a double quote in a |
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1092 string, use backslash. Similarly a double backslash is used to get a literal backslash. For example ab\"c\\d is the string ab"c\d. |
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1093 |
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1094 Comparison operators are evaluated as a match being 1 and a mismatch being 0, thus "(2 > 1) + (3 < 5)" evaluates as 2. All comparisons involving undefined (null) values are deemed to be false. |
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1095 |
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1096 The variables are where the file format specifics are accessed from the expression. The variables correspond to SAM fields, for example to find paired |
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1097 alignments with high mapping quality and a very large insert size, we may use the expression "mapq >= 30 && (tlen >= 100000 || tlen <= -100000)". Valid |
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1098 variable names and their data types are: |
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1099 |
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1100 :: |
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1101 |
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1102 endpos int Alignment end position (1-based) |
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1103 flag int Combined FLAG field |
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1104 flag.paired int Single bit, 0 or 1 |
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1105 flag.proper_pair int Single bit, 0 or 2 |
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1106 flag.unmap int Single bit, 0 or 4 |
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1107 flag.munmap int Single bit, 0 or 8 |
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1108 flag.reverse int Single bit, 0 or 16 |
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1109 flag.mreverse int Single bit, 0 or 32 |
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1110 flag.read1 int Single bit, 0 or 64 |
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1111 flag.read2 int Single bit, 0 or 128 |
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1112 flag.secondary int Single bit, 0 or 256 |
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1113 flag.qcfail int Single bit, 0 or 512 |
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1114 flag.dup int Single bit, 0 or 1024 |
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1115 flag.supplementary int Single bit, 0 or 2048 |
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1116 hclen int Number of hard-clipped bases |
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1117 library string Library (LB header via RG) |
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1118 mapq int Mapping quality |
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1119 mpos int Synonym for pnext |
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1120 mrefid int Mate reference number (0 based) |
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1121 mrname string Synonym for rnext |
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1122 ncigar int Number of cigar operations |
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1123 pnext int Mate's alignment position (1-based) |
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1124 pos int Alignment position (1-based) |
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1125 qlen int Alignment length: no. query bases |
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1126 qname string Query name |
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1127 qual string Quality values (raw, 0 based) |
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1128 refid int Integer reference number (0 based) |
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1129 rlen int Alignment length: no. reference bases |
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1130 rname string Reference name |
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1131 rnext string Mate's reference name |
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1132 sclen int Number of soft-clipped bases |
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1133 seq string Sequence |
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1134 tlen int Template length (insert size) |
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1135 [XX] int / string XX tag value |
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1136 |
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1137 |
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1138 Flags are returned either as the whole flag value or by checking for a single bit. Hence the filter expression flag.dup is equivalent to flag & 1024. |
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1139 |
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1140 "qlen" and "rlen" are measured using the CIGAR string to count the number of query (sequence) and reference bases consumed. Note "qlen" may not exactly |
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1141 match the length of the "seq" field if the sequence is "*". |
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1142 |
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1143 "sclen" and "hclen" are the number of soft and hard-clipped bases respectively. The formula "qlen-sclen" gives the number of sequence bases used in the |
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1144 alignment, distinguishing between global alignment and local alignment length. |
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1145 |
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1146 "endpos" is the (1-based inclusive) position of the rightmost mapped base of the read, as measured using the CIGAR string, and for mapped reads is |
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1147 equivalent to "pos+rlen-1". For unmapped reads, it is the same as "pos". |
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1148 |
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1149 Reference names may be matched either by their string forms ("rname" and "mrname") or as the Nth @SQ line (counting from zero) as stored in BAM using |
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1150 "tid" and "mtid" respectively. |
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1151 |
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1152 Auxiliary tags are described in square brackets and these expand to either integer or string as defined by the tag itself (XX:Z:string or XX:i:int). |
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1153 For example [NM]>=10 can be used to look for alignments with many mismatches and [RG]=~"grp[ABC]-" will match the read-group string. |
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1154 |
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1155 If no comparison is used with an auxiliary tag it is taken simply to be a test for the existence of that tag. So [NM] will return any record containing |
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1156 an NM tag, even if that tag is zero (NM:i:0). In htslib <= 1.15 negating this with ![NM] gave misleading results as it was true if the tag did not exist |
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1157 or did exist but was zero. Now this is strictly does-not-exist. An explicit exists([NM]) and !exists([NM]) function has also been added to make |
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1158 this intention clear. |
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1159 |
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1160 Similarly in htslib <= 1.15 using [NM]!=0 was true both when the tag existed and was not zero as well as when the tag did not exist. From 1.16 onwards |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1161 all comparison operators are only true for tags that exist, so [NM]!=0 works as expected. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1162 |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1163 Some simple functions are available to operate on strings. These treat the strings as arrays of bytes, permitting their length, minimum, maximum and |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1164 average values to be computed. These are useful for processing Quality Scores. |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1165 |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1166 :: |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1167 |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1168 length(x) Length of the string (excluding nul char) |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1169 min(x) Minimum byte value in the string |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1170 max(x) Maximum byte value in the string |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1171 avg(x) Average byte value in the string |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1172 |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1173 |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1174 Note that "avg" is a floating point value and it may be NAN for empty strings. This means that "avg(qual)" does not produce an error for records that |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1175 have both seq and qual of "*". NAN values will fail any conditional checks, so e.g. "avg(qual) > 20" works and will not report these records. NAN also |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1176 fails all equality, < and > comparisons, and returns zero when given as an argument to the exists function. It can be negated with !x in which case it |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1177 becomes true. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1178 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1179 Functions that operate on both strings and numerics: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1180 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1181 :: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1182 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1183 exists(x) True if the value exists (or is explicitly true). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1184 default(x,d) Value x if it exists or d if not. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1185 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1186 Functions that apply only to numeric values: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1187 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1188 :: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1189 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1190 qrt(x) Square root of x |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1191 og(x) Natural logarithm of x |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1192 ow(x, y) Power function, x to the power of y |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1193 xp(x) Base-e exponential, equivalent to pow(e,x) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1194 |
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0
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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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1195 </help> |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1196 <expand macro="citations"/> |
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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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1197 </tool> |