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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:02:40 +0000
parents fd87401a3da6
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9a12e8643fc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="samtools_idxstats" name="Samtools idxstats" version="2.0.4" profile="@PROFILE@">
2
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2 <description>reports stats of the BAM index file</description>
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3 <macros>
2
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4 <import>macros.xml</import>
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5 </macros>
2
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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"/>
0
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9 <command><![CDATA[
4
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10 @ADDTHREADS@
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11 @PREPARE_IDX@
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12 samtools idxstats -@ \$addthreads infile > '${output}'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="bam,cram" label="BAM file" />
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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19 </outputs>
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20 <tests>
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21 <!-- test from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2556 -->
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22 <test>
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23 <param name="input" value="test_input_1_a.bam" ftype="bam" />
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24 <output name="output" file="test_input_1_a.bam.expected" compare="diff" ftype="tabular" />
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25 </test>
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26 <!-- test from original tool -->
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27 <test>
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28 <param name="input" value="phiX.bam" ftype="bam" />
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29 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 **What it does**
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35 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
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37 Input is a sorted and indexed BAM file, the output is tabular with
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38 four columns (one row per reference sequence plus a final line for
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39 unmapped reads)::
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41 Column Description
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42 ------ -----------------------------
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43 1 Reference sequence identifier
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44 2 Reference sequence length
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45 3 Number of mapped reads
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46 4 Number of placed but unmapped reads
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47 (typically unmapped partners of mapped reads)
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48
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49 ------
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51 **Example** output from a *de novo* assembly::
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53 contig_1 170035 98397 0
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54 contig_2 403835 199564 0
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55 contig_3 553102 288189 0
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56 ... ... ... ...
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57 contig_603 653 50 0
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58 contig_604 214 6 0
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59 \* 0 0 50320
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60
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61 In this example there were 604 contigs, each with one line in the output table,
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62 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
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63 In this BAM file, the final column was otherwise zero.
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64
5
fd87401a3da6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
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66 The results of samtools ixdstats can be visualized with MultiQC.
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67
0
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68 ------
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70 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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71 ]]></help>
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72 <expand macro="citations"/>
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73 </tool>