Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_add-read-counts.xml @ 16:7e5b96d45f8d draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit c6608bd5256e5c54cb2e01be6c184da0d2b08a7c-dirty
author yhoogstrate
date Thu, 19 May 2016 05:41:48 -0400
parents c690aa928d3d
children 3fbde4864e00
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1 <tool id="smf_utils_add-read-counts" name="add-read-counts" version="@VERSION@-0">
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2 <description>Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.7.10">python</requirement>
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10 <requirement type="package" version="1.9">numpy</requirement>
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11 <requirement type="package" version="0.8.2.1">pysam</requirement>
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12 <requirement type="package" version="2.0.0">segmentation-fold-utils</requirement>
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13 </requirements>
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14 <expand macro="stdio" />
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16 <version_command>@VERSION_COMMAND_UTILS@</version_command>
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18 <command><![CDATA[
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19 ln -f -s '${bam_input_file.metadata.bam_index}' '${bam_input_file}.bai' &&
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21 segmentation-fold-utils
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22 add-read-counts
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23 --regex '${regex.replace("'","\\'")}'
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24 '$dbn_input_file'
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25 '$bam_input_file'
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26 '$dbn_output_file'
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27 ]]></command>
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29 <inputs>
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30 <param name="dbn_input_file"
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31 type="data"
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32 format="dbn,txt,text"
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33 label="Input DBN file"
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34 help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
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35 <param name="bam_input_file"
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36 type="data"
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37 format="bam"
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38 label="Input BAM file"/>
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39 <param name="regex"
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40 type="text"
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41 argument="--regex"
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42 value='>.*?(chr[^:]):([0-9]+)-([0-9]+)'
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43 label="Regex to capture the targeted location in DBN file"
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44 help="Do not change this value unless you're using customized software in the pipeline - default: '>.*?(chr[^:]):([0-9]+)-([0-9]+)'" />
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45 </inputs>
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46
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47 <outputs>
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48 <data name="dbn_output_file"
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49 format="dbn"
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50 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name}"/>
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="dbn_input_file" value="DBNFile.test_01.in.dbn" ftype="dbn"/>
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56 <param name="bam_input_file" value="DBNFile.test_01.in.bam" ftype="bam"/>
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57 <param name="regex" value='>.*?(chr[^:]):([0-9]+)-([0-9]+)'/>
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59 <output name="dbn_output_file">
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60 <assert_contents>
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61 <has_line_matching expression="&gt;chr1:10-21 x unknown-01 \(aligned reads .*?: 20\)"/>
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62 <has_line line="GGGGAAACCCC"/>
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63 <has_line line="((((...))))&#009;((.((.)).))&#009;-2.5"/>
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64 <has_line line="((.((.)).))&#009;(((((.)))))&#009;-3.5"/>
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65
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66 <has_line_matching expression="&gt;chr1:25-36 x unknown-01 \(aligned reads.*?: 1\)"/>
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67 <has_line line="AAAAAAAAAAA"/>
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68
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69 <has_line_matching expression="&gt;chr1:45-56 x unknown-01 \(aligned reads .*?: 2\)"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74
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75 <help><![CDATA[
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76 This is an utility of the segmentation-fold package
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77 ]]></help>
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78
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79 <expand macro="citations" />
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80 </tool>