Mercurial > repos > iuc > samtools_coverage
annotate samtools_coverage.xml @ 2:8a477224dfee draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
author | iuc |
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date | Wed, 31 May 2023 17:15:17 +0000 |
parents | ae36fab06bc2 |
children | c4ff13d2aab3 |
rev | line source |
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2
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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changeset
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1 <tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
parents:
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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"
iuc
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6 <expand macro="requirements"/> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
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7 <expand macro="stdio"/> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
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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"
iuc
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9 <command><![CDATA[ |
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8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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changeset
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10 #if $condition_input.input_pooling == "No": |
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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11 @PREPARE_IDX@ |
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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12 #else: |
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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13 @PREPARE_IDX_MULTIPLE@ |
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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14 #end if |
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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"
iuc
parents:
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15 samtools coverage |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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16 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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17 #if $condition_input.input_pooling == "Yes": |
2
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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18 ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input_bams] ) } |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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19 #else |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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20 '$condition_input.input' |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
parents:
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21 #end if |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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22 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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23 -l $additional_options.min_read_length |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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24 -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"
iuc
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25 -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"
iuc
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26 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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27 #set $filter = $additional_options.required_flags |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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28 @FLAGS@ |
2
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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29 --rf $flags |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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30 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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31 #set $filter = $additional_options.skipped_flags |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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32 @FLAGS@ |
2
8a477224dfee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 3a5a4ad75547c6c27430d85e6ddf3c2ff1ece0ba
iuc
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33 --ff $flags |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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34 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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35 #if $condition_histogram.histogram_select == "yes" |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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36 -m |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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37 -w $condition_histogram.n_bins |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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38 #if $condition_histogram.region != "": |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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39 -r '$condition_histogram.region' |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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40 #end if |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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41 #end if |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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42 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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43 -o '$output' |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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44 ]]></command> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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45 <inputs> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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46 <conditional name="condition_input"> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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47 <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"
iuc
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48 <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"
iuc
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49 <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"
iuc
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50 </param> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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51 <when value="No" > |
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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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52 <param name="input" type="data" format="bam" label="BAM file"/> |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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53 </when> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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54 <when 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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55 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> |
0
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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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"
iuc
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57 </conditional> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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58 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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59 <section name="additional_options" title="Additional Options" expanded="true"> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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60 <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"
iuc
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61 <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"
iuc
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62 <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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63 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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64 <param name="required_flags" argument="--rf" type="select" multiple="True" label="Require that these flags are set"> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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65 <expand macro="flag_options" /> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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66 </param> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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67 |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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68 <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"
iuc
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69 <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"
iuc
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70 </param> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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71 </section> |
90f2dd176d80
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
iuc
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72 |
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 <conditional name="condition_histogram"> |
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74 <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output"> |
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75 <option value="no" selected="true">No</option> |
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76 <option value="yes">Yes</option> |
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77 </param> |
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78 <when value="yes"> |
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79 <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" /> |
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80 <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." /> |
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81 </when> |
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82 <when value="no" /> |
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83 </conditional> |
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84 </inputs> |
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85 |
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86 <outputs> |
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87 <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" /> |
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88 </outputs> |
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89 |
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90 <tests> |
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91 <test> |
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92 <param name="input" value="test_1.bam" ftype="bam" /> |
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93 <output name="output" file="results_1.tabular" ftype="tabular" /> |
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94 </test> |
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95 <test> |
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96 <param name="input" value="test_1.bam" ftype="bam" /> |
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97 <param name="histogram_select" value="yes" /> |
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98 <param name="n_bins" value="50" /> |
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99 <output name="output" file="results_2.txt" ftype="tabular" /> |
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100 </test> |
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101 <test> |
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102 <param name="input_pooling" value="Yes" /> |
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103 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> |
0
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104 <param name="histogram_select" value="yes" /> |
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105 <param name="n_bins" value="100" /> |
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106 <output name="output" file="results_3.txt" ftype="tabular" /> |
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107 </test> |
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108 </tests> |
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109 <help><![CDATA[ |
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110 **What it does** |
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111 |
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112 This tool runs the ``samtools coverage`` command. |
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113 |
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114 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. |
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115 |
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116 The tabulated form uses the following headings: |
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117 |
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118 - rname Reference name / chromosome |
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119 - startpos Start position |
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120 - endpos End position (or sequence length) |
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121 - numreads Number reads aligned to the region (after filtering) |
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122 - covbases Number of covered bases with depth >= 1 |
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123 - coverage Proportion of covered bases [0..1] |
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124 - meandepth Mean depth of coverage |
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125 - meanbaseq Mean baseQ in covered region |
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126 - meanmapq Mean mapQ of selected reads |
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127 |
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128 ]]></help> |
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129 <expand macro="citations"/> |
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130 </tool> |