Mercurial > repos > iuc > samtools_coverage

annotate samtools_coverage.xml @ 3:c4ff13d2aab3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
author iuc
date Thu, 29 Jun 2023 10:40:07 +0000
parents 8a477224dfee
children
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c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
iuc
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1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>computes the depth at each position or region</description>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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3 <macros>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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4 <import>macros.xml</import>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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5 </macros>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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9 <command><![CDATA[
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10 #if $condition_input.input_pooling == "No":
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c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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11 #set $input = $condition_input.input
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12 @PREPARE_IDX@
8a477224dfee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
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13 #else:
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c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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14 #set $input_bams = $condition_input.input_bams
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15 @PREPARE_IDX_MULTIPLE@
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16 #end if
0
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17 samtools coverage
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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19 #if $condition_input.input_pooling == "Yes":
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c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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20 ${ ' '.join( [ "'%s'" % $i for $i, $x in enumerate($condition_input.input_bams)]) }
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21 #else
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22 infile
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23 #end if
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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24
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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25 -l $additional_options.min_read_length
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26 -q $additional_options.min_mq
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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27 -Q $additional_options.min_bq
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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29 #set $filter = $additional_options.required_flags
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30 @FLAGS@
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31 --rf $flags
0
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33 #set $filter = $additional_options.skipped_flags
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34 @FLAGS@
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35 --ff $flags
0
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36
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c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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37 #if $additional_options.region != "":
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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38 -r '$additional_options.region'
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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39 #end if
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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40
0
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41 #if $condition_histogram.histogram_select == "yes"
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42 -m
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43 -w $condition_histogram.n_bins
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44 #end if
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45
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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46 -o '$output'
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47 ]]></command>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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48 <inputs>
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49 <conditional name="condition_input">
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50 <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" >
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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51 <option value="No" selected="True">No</option>
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52 <option value="Yes">Yes</option>
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53 </param>
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54 <when value="No" >
2
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55 <param name="input" type="data" format="bam" label="BAM file"/>
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56 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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57 <when value="Yes">
2
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58 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/>
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59 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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60 </conditional>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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61
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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62 <section name="additional_options" title="Additional Options" expanded="true">
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63 <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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64 <param name="min_mq" argument="-q" type="integer" min="0" value="0" label="Minimum mapping quality" help="Minimum mapping quality for an alignment to be used (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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65 <param name="min_bq" argument="-Q" type="integer" min="0" value="0" label="Minimum base quality" help="Minimum base quality for a base to be considered (Default = 0)" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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66
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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67 <param name="required_flags" argument="--rf" type="select" multiple="True" label="Require that these flags are set">
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68 <expand macro="flag_options" />
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69 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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70
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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71 <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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72 <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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73 </param>
3
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74 <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." >
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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75 <sanitizer invalid_char="">
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76 <valid initial="string.ascii_letters,string.digits">
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77 <add value=":" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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78 <add value="-" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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79 <add value="_" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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80 </valid>
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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81 </sanitizer>
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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82 </param>
0
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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83 </section>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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84
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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85 <conditional name="condition_histogram">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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86 <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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87 <option value="no" selected="true">No</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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88 <option value="yes">Yes</option>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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89 </param>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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90 <when value="yes">
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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91 <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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92 </when>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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93 <when value="no" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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94 </conditional>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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95 </inputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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96
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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97 <outputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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98 <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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99 </outputs>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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100
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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101 <tests>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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102 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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103 <param name="input" value="test_1.bam" ftype="bam" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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104 <output name="output" file="results_1.tabular" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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105 </test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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106 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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107 <param name="input" value="test_1.bam" ftype="bam" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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108 <param name="histogram_select" value="yes" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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109 <param name="n_bins" value="50" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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110 <output name="output" file="results_2.txt" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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111 </test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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112 <test>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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113 <param name="input_pooling" value="Yes" />
2
8a477224dfee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
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114 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
0
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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115 <param name="histogram_select" value="yes" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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116 <param name="n_bins" value="100" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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117 <output name="output" file="results_3.txt" ftype="tabular" />
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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118 </test>
3
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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119 <test><!-- test with a region (requires index) -->
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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120 <param name="input" value="test_1.bam" ftype="bam" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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121 <param name="region" value="ref1" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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122 <output name="output" file="results_4.tabular" ftype="tabular" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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123 </test>
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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124 <test><!-- test with pooled BAMs and a region -->
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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125 <param name="input_pooling" value="Yes" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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126 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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127 <param name="region" value="ref2" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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128 <output name="output" file="results_5.tabular" ftype="tabular" />
c4ff13d2aab3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 69ce9eb437322f15750e532c6e9586e4e17fe424
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129 </test>
0
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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130 </tests>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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131 <help><![CDATA[
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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132 **What it does**
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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133
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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134 This tool runs the ``samtools coverage`` command.
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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135
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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136 Computes the depth at each position or region and draws an ASCII-art histogram or tabulated text. If you select to pool the bam files, then it calculates coverage for the combined files.
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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137
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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138 The tabulated form uses the following headings:
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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139
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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140 - rname Reference name / chromosome
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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141 - startpos Start position
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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142 - endpos End position (or sequence length)
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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143 - numreads Number reads aligned to the region (after filtering)
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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144 - covbases Number of covered bases with depth >= 1
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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145 - coverage Proportion of covered bases [0..1]
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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146 - meandepth Mean depth of coverage
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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147 - meanbaseq Mean baseQ in covered region
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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148 - meanmapq Mean mapQ of selected reads
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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149
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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150 ]]></help>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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151 <expand macro="citations"/>
90f2dd176d80 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
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152 </tool>