Mercurial > repos > iuc > ngsutils_bam_filter
annotate bam_filter.xml @ 2:7a68005de299 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author | iuc |
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date | Sun, 27 Nov 2016 15:01:21 -0500 |
parents | 8187a729d9f4 |
children | 9b9ae5963d3c |
rev | line source |
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1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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1 <tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@.1"> |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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2 <description>Removes reads from a BAM file based on criteria</description> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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3 <macros> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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4 <import>macros.xml</import> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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5 </macros> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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6 <expand macro="requirements" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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7 <expand macro="stdio" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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8 <expand macro="version" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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9 <command><![CDATA[ |
1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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10 |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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11 ## If the tool is executed with no filtering option, |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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12 ## the default parameters simply copy over the input file |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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13 if grep -q "\w" ${parameters}; |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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14 then |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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15 $__tool_directory__/filter.py |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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16 $infile |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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17 $outfile |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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18 `cat ${parameters}`; |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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19 else |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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20 cp $infile $outfile; |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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21 fi |
1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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22 |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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23 ]]> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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24 </command> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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changeset
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25 <configfiles> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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26 <configfile name="parameters"> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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27 <![CDATA[ |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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28 #if $minlen: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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29 -minlen $minlen |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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30 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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31 #if $maxlen |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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32 -maxlen $maxlen |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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33 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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34 $mapped |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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35 $unmapped |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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36 $properpair |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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37 $noproperpair |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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38 #if $mask: |
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8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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39 -mask ${mask} |
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4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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40 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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41 #if int($uniq) > -1: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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42 -uniq |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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43 #if int($uniq) > 0: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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44 $uniq |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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45 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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46 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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47 $uniq_start |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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48 #if $mismatch: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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49 -mismatch $mismatch |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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50 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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51 $nosecondary |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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52 $noqcfail |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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53 $nopcrdup |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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54 #if $excludebed: |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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55 -excludebed ${excludebed} $ignore_strand |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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56 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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57 #if $includebed: |
1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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58 -includebed ${includebed} $ignore_strand |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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59 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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60 #if $includeref: |
1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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61 -includeref ${includeref} |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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62 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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63 #if $excluderef: |
1
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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64 -excluderef ${excluderef} |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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65 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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66 #if $maximum_mismatch_ratio |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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67 -maximum_mismatch_ratio $maximum_mismatch_ratio |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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68 #end if |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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69 ]]> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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70 </configfile> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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71 </configfiles> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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72 <inputs> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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73 <param name="infile" type="data" format="bam" label="Select BAM dataset" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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74 <param argument="-minlen" type="integer" value="" optional="True" min="0" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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75 label="Remove reads that are smaller than" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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76 help="in bp"/> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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77 <param argument="-maxlen" type="integer" value="" optional="True" min="0" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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78 label="Remove reads that are larger than" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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79 help="in bp"/> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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80 <param argument="-mapped" truevalue="-mapped" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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81 label="Keep only mapped reads" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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82 help="" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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83 <param argument="-unmapped" truevalue="-unmapped" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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84 label="Keep only unmapped reads" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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changeset
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85 help="" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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changeset
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86 <param argument="-properpair" truevalue="-properpair" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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87 label="Keep only properly paired reads" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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88 help="both mapped, correct orientation, flag set in BAM" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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89 <param argument="-noproperpair" truevalue="-noproperpair" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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90 label="Discard properly paired reads" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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91 help="" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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92 <param argument="-mask" type="text" value="" optional="True" label="Remove reads that match the mask" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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93 help="e.g. 0x400, 0x2" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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94 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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95 <param argument="-uniq" type="integer" value="-1" optional="True" min="-1" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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changeset
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96 label="Remove reads that have the same sequence" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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97 help="up to the Nth nucleotide starting from the 5prime end. -1 means do not filter, 0 means check along the entire read, |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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98 10 would make filter reads that are unique over the first 10 nucleotides."/> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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99 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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100 <param argument="-uniq_start" truevalue="-uniq_start" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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101 label="Remove reads that start at the same position" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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102 help="Use only for low-coverage samples" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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103 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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104 <param argument="-mismatch" type="integer" value="" optional="True" min="0" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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105 label="Remove reads with that many mismatches" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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106 help="Indels always counts as 1 regardless of length. Requires NM tag to be set."/> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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107 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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108 <param argument="-nosecondary" truevalue="-nosecondary" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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109 label="Remove secondary alignment reads" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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110 help="Remove reads flagged with 0x100" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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111 <param argument="-noqcfail" truevalue="-noqcfail" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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112 label="Remove reads that do not pass the quality control" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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113 help="Remove reads flagged with 0x200" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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114 <param argument="-nopcrdup" truevalue="-nopcrdup" type="boolean" falsevalue="" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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115 label="Remove reads that are marked as PCR dupicates " |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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116 help="Remove reads flagged with 0x400" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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117 |
4e4e4093d65d
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118 <param argument="-excludebed" type="data" optional="True" format="bed" label="Remove reads that are in any of the regions" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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119 <param argument="-includebed" type="data" optional="True" format="bed" label="Remove reads that are NOT any of the regions" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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120 <param name="ignore_strand" truevalue="nostrand" type="boolean" falsevalue="" |
1
8187a729d9f4
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121 label="Strand information from BED file is ignored" |
8187a729d9f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit bbabad202be09c91e66c94bcbfd057e49f57c841
iuc
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122 help="Affects -excludebed and -includebed." /> |
0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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123 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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124 <param argument="-includeref" type="text" value="" optional="True" label="Exclude reads NOT mapped to a reference" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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125 help="" /> |
4e4e4093d65d
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126 <param argument="-excluderef" type="text" value="" optional="True" label="Exclude reads mapped to a particular reference" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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127 help="e.g. chrM, or _dup chromosomes" /> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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128 |
4e4e4093d65d
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129 <param argument="-maximum_mismatch_ratio" type="float" value="" optional="True" min="0.0" max="1.0" |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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130 label="Filter by maximum mismatch ratio" |
4e4e4093d65d
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131 help="fraction of length"/> |
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132 |
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133 </inputs> |
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134 <outputs> |
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135 <data format="bam" name="outfile" /> |
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136 </outputs> |
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137 <tests> |
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138 <test> |
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139 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
4e4e4093d65d
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140 <param name="minlen" value="100"/> |
4e4e4093d65d
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141 <param name="maximum_mismatch_ratio" value="0.02"/> |
4e4e4093d65d
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142 <output name="outfile" file="ngsutils_bam_filter_result1.bam" ftype="bam" /> |
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143 </test> |
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144 <test> |
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145 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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146 <param name="minlen" value="250"/> |
4e4e4093d65d
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147 <param name="properpair" value="True"/> |
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148 <output name="outfile" file="ngsutils_bam_filter_result2.bam" ftype="bam" /> |
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149 </test> |
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150 <test> |
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151 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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152 <param name="minlen" value="100"/> |
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153 <param name="nosecondary" value="True"/> |
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154 <param name="noqcfail" value="True"/> |
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155 <param name="nopcrdup" value="True"/> |
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156 <output name="outfile" file="ngsutils_bam_filter_result3.bam" ftype="bam" /> |
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157 </test> |
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158 <test> |
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159 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
1
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160 <output name="outfile" file="ngsutils_bam_filter_input4.bam" ftype="bam" /> |
0
4e4e4093d65d
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161 </test> |
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162 <test> |
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163 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
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164 <param name="mask" value="0x40"/> |
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165 <output name="outfile" file="ngsutils_bam_filter_result5.bam" ftype="bam" /> |
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166 </test> |
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167 <test> |
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168 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/> |
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169 <param name="excludebed" value="exclude.bed" ftype="bed"/> |
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170 <param name="ignore_strand" value="True" /> |
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171 <output name="outfile" file="ngsutils_bam_filter_result6.bam" ftype="bam" /> |
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172 </test> |
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173 </tests> |
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174 <help><![CDATA[ |
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175 Removes reads from a BAM file based on criteria. |
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176 |
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177 Given a BAM file, this tool will discard reads that did not meet the selected filtering criteria |
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178 The output is another BAM file with the reads not matching the criteria removed. |
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179 |
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180 Note: this does not adjust tag values reflecting any filtering. (for example: |
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181 if a read mapped to two locations (IH:i:2), and one was removed by |
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182 filtering, the IH:i tag would still read IH:i:2). |
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183 |
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184 Currently, the available filters are: |
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185 |
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186 +--------------------------------+-------------------------------------------------+ |
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187 | Agument | Description | |
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188 +================================+=================================================+ |
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189 | -minlen val | Remove reads that are smaller than {val} | |
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190 +--------------------------------+-------------------------------------------------+ |
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191 | -maxlen val | Remove reads that are larger than {val} | |
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192 +--------------------------------+-------------------------------------------------+ |
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193 | -mapped | Keep only mapped reads | |
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194 +--------------------------------+-------------------------------------------------+ |
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195 | -unmapped | Keep only unmapped reads | |
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196 +--------------------------------+-------------------------------------------------+ |
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197 | -properpair | Keep only properly paired reads (both mapped, | |
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198 | | correct orientation, flag set in BAM) | |
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199 +--------------------------------+-------------------------------------------------+ |
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200 | -noproperpair | Keep only not-properly paired reads | |
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201 +--------------------------------+-------------------------------------------------+ |
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202 | -mask bitmask | Remove reads that match the mask (e.g. 0x400) | |
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203 +--------------------------------+-------------------------------------------------+ |
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204 | -uniq {length} | Remove reads that are have the same sequence | |
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205 | | Note: BAM file should be sorted | |
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206 | | (up to an optional length) | |
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207 +--------------------------------+-------------------------------------------------+ |
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208 | -uniq_start | Remove reads that start at the same position | |
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209 | | Note: BAM file should be sorted | |
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210 | | (Use only for low-coverage samples) | |
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211 +--------------------------------+-------------------------------------------------+ |
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212 |-mismatch num | Number of mismatches or indels | |
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213 | | indel always counts as 1 regardless of length | |
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214 | | (requires NM tag in reads) | |
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215 +--------------------------------+-------------------------------------------------+ |
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216 |-nosecondary | Remove reads that have the 0x100 flag set | |
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217 +--------------------------------+-------------------------------------------------+ |
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218 |-noqcfail | Remove reads that have the 0x200 flag set | |
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219 +--------------------------------+-------------------------------------------------+ |
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220 |-nopcrdup | Remove reads that have the 0x400 flag set | |
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221 +--------------------------------+-------------------------------------------------+ |
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222 |-excludebed file.bed {nostrand} | Remove reads that are in any of the regions | |
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223 | | from the given BED file. If 'nostrand' is given,| |
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224 | | strand information from the BED file is ignored.| |
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225 +--------------------------------+-------------------------------------------------+ |
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226 |-includebed file.bed {nostrand} | Remove reads that are NOT any of the regions | |
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227 | | from the given BED file. If 'nostrand' is given,| |
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228 | | strand information from the BED file is ignored.| |
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229 | | Note: If this is a large dataset, use | |
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230 | | "bamutils extract" instead. | |
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231 +--------------------------------+-------------------------------------------------+ |
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232 | -includeref refname | Exclude reads NOT mapped to a reference | |
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233 +--------------------------------+-------------------------------------------------+ |
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234 | -excluderef refname | Exclude reads mapped to a particular reference | |
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235 | | (e.g. chrM, or _dup chromosomes) | |
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236 +--------------------------------+-------------------------------------------------+ |
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237 ]]> |
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238 </help> |
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239 </tool> |