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annotate samtools_idxstats.xml @ 3:20fea18b2830 draft

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author iuc
date Thu, 27 Sep 2018 08:58:41 -0400
parents e726bb429392
children 56838051b673
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1 <tool id="samtools_idxstats" name="Samtools idxstats" version="2.0.2">
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2 <description>reports stats of the BAM index file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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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"/>
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9 <command><![CDATA[
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10 @PREPARE_IDX@
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11 samtools idxstats infile > '${output}'
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12 ]]></command>
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13 <inputs>
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14 <param name="input" type="data" format="bam,cram" label="BAM file" />
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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18 </outputs>
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19 <tests>
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20 <!-- test from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2556 -->
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21 <test>
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22 <param name="input" value="test_input_1_a.bam" ftype="bam" />
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23 <output name="output" file="test_input_1_a.bam.expected" compare="diff" ftype="tabular" />
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24 </test>
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25 <!-- test from original tool -->
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26 <test>
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27 <param name="input" value="phiX.bam" ftype="bam" />
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28 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32 **What it does**
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a5f8ee692d38 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
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36 Input is a sorted and indexed BAM file, the output is tabular with
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37 four columns (one row per reference sequence plus a final line for
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38 unmapped reads)::
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40 Column Description
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41 ------ -----------------------------
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42 1 Reference sequence identifier
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43 2 Reference sequence length
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44 3 Number of mapped reads
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45 4 Number of placed but unmapped reads
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46 (typically unmapped partners of mapped reads)
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48 ------
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50 **Example** output from a *de novo* assembly::
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52 contig_1 170035 98397 0
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53 contig_2 403835 199564 0
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54 contig_3 553102 288189 0
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55 ... ... ... ...
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56 contig_603 653 50 0
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57 contig_604 214 6 0
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58 \* 0 0 50320
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60 In this example there were 604 contigs, each with one line in the output table,
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61 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
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62 In this BAM file, the final column was otherwise zero.
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64 ------
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66 Peter J.A. Cock (2013), `Galaxy wrapper <https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats>`_ for the samtools idxstats command
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67 ]]></help>
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68 <expand macro="citations"/>
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69 </tool>