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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:17:04 -0400
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e726bb429392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="samtools_idxstats" name="IdxStats" version="2.0.1">
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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 ln -f -s '${input.metadata.bam_index}' '${input}.bai' &&
e726bb429392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 samtools idxstats '${input}' > '${output}'
e726bb429392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="bam" 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>
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22 <param name="input" value="phiX.bam" ftype="bam" />
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23 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
a5f8ee692d38 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 **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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29 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
a5f8ee692d38 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 Input is a sorted and indexed BAM file, the output is tabular with
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32 four columns (one row per reference sequence plus a final line for
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33 unmapped reads)::
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35 Column Description
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36 ------ -----------------------------
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37 1 Reference sequence identifier
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38 2 Reference sequence length
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39 3 Number of mapped reads
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40 4 Number of placed but unmapped reads
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41 (typically unmapped partners of mapped reads)
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43 ------
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45 **Example** output from a *de novo* assembly::
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47 contig_1 170035 98397 0
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48 contig_2 403835 199564 0
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49 contig_3 553102 288189 0
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50 ... ... ... ...
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51 contig_603 653 50 0
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52 contig_604 214 6 0
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53 \* 0 0 50320
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54
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55 In this example there were 604 contigs, each with one line in the output table,
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56 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
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57 In this BAM file, the final column was otherwise zero.
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59 ------
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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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61 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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62 ]]></help>
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63 <expand macro="citations"/>
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64 </tool>