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1 <tool id="samtools_idxstats" name="IdxStats" version="2.0">
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2 <description>tabulate mapping statistics for BAM dataset</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"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command><![CDATA[
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10 if [ ! -f "${input}.bai" ] ; then
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11 ln -s "${input}" input.bam ;
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12 samtools sort -o sorted.bam -O bam -T sts "${input}" ;
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13 samtools index sorted.bam ;
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14 samtools idxstats sorted.bam > "${output}" ;
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15 else
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16 samtools idxstats "${input}" > "${output}" ;
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17 fi]]>
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" format="bam" label="BAM file" />
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
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24 </outputs>
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25 <tests>
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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>
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32 <![CDATA[
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33 **What it does**
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34
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35 Runs the ``samtools idxstats`` command. It retrieves and prints stats in the index file.
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36
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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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40
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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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50
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51 **Example** output from a *de novo* assembly::
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52
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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
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62 In this example there were 604 contigs, each with one line in the output table,
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63 plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
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64 In this BAM file, the final column was otherwise zero.
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65
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66 ------
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67
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68 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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69 ]]>
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70 </help>
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71 <expand macro="citations"></expand>
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72 </tool>
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