Mercurial > repos > peterjc > samtools_idxstats
annotate tools/samtools_idxstats/samtools_idxstats.xml @ 1:8945bad80f4a draft
v0.0.4; internal changes for packaging
author | peterjc |
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date | Wed, 13 May 2015 10:35:50 -0400 |
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1 | 1 <tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.4"> |
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2 <description>samtools idxstats</description> |
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3 <requirements> |
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4 <requirement type="binary">samtools</requirement> |
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5 <requirement type="package" version="0.1.19">samtools</requirement> |
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6 </requirements> |
1 | 7 <stdio> |
8 <!-- Assume anything other than zero is an error --> | |
9 <exit_code range="1:" /> | |
10 <exit_code range=":-1" /> | |
11 </stdio> | |
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12 <version_command interpreter="python">samtools_idxstats.py --version</version_command> |
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13 <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command> |
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14 <inputs> |
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15 <param name="input_bam" type="data" format="bam" label="Input BAM file" /> |
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16 </inputs> |
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17 <outputs> |
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18 <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" /> |
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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_bam" value="ex1.bam" ftype="bam" /> |
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23 <output name="out_tabular" file="ex1.idxstats.tabular" ftype="tabular" /> |
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24 </test> |
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25 </tests> |
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26 <help> |
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27 **What it does** |
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28 |
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29 This tool runs the ``samtools idxstats`` command in the SAMtools toolkit. |
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30 |
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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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34 |
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35 ====== ================================================================================= |
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36 Column Description |
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37 ------ --------------------------------------------------------------------------------- |
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38 1 Reference sequence identifier |
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39 2 Reference sequence length |
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40 3 Number of mapped reads |
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41 4 Number of placed but unmapped reads (typically unmapped partners of mapped reads) |
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42 ====== ================================================================================= |
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43 |
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44 Example output from a *de novo* assembly: |
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45 |
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46 ========== ====== ====== ===== |
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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 |
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56 In this example there were 604 contigs, each with one line in the output table, |
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57 plus the final row (labelled with an asterisk) representing 50320 unmapped reads. |
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58 In this BAM file, the final column was otherwise zero. |
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59 |
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60 |
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61 **Citation** |
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62 |
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63 If you use this Galaxy tool in work leading to a scientific publication please |
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64 cite: |
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65 |
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66 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools. |
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67 Bioinformatics 25(16), 2078-9. |
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68 http://dx.doi.org/10.1093/bioinformatics/btp352 |
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69 |
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70 Peter J.A. Cock (2013), Galaxy wrapper for the samtools idxstats command |
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71 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats |
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72 |
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73 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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74 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats |
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75 </help> |
1 | 76 <citations> |
77 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
78 </citations> | |
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79 </tool> |