Mercurial > repos > yhoogstrate > segmentation_fold

annotate utils_add-read-counts.xml @ 26:660c25c66c8a draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
author erasmus-medical-center
date Fri, 24 Feb 2017 04:18:08 -0500
parents 44330a54b8eb
children
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1 <tool id="smf_utils_add-read-counts" name="add-read-counts" version="@VERSION@-3">
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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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7
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 ln -f -s '${bam_input_file.metadata.bam_index}' '${bam_input_file}.bai' &&
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14 segmentation-fold-utils
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15 add-read-counts
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16 --regex '${regex.replace("'","\\'")}'
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17 '$dbn_input_file'
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18 '$bam_input_file'
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19 '$dbn_output_file'
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20 ]]></command>
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22 <inputs>
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23 <param name="dbn_input_file"
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24 type="data"
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25 format="dbn,txt,text"
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26 label="Input DBN file"
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27 help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/>
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28 <param name="bam_input_file"
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29 type="data"
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30 format="bam"
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31 label="Input BAM file"/>
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32 <param name="regex"
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33 type="text"
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34 argument="--regex"
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35 value='>.*?(chr[^:]):([0-9]+)-([0-9]+)'
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36 label="Regex to capture the targeted location in DBN file"
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37 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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38 </inputs>
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40 <outputs>
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41 <data name="dbn_output_file"
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42 format="dbn"
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43 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name}"/>
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44 </outputs>
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45
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46 <tests>
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47 <test>
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48 <param name="dbn_input_file" value="DBNFile.test_01.in.dbn" ftype="dbn"/>
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49 <param name="bam_input_file" value="DBNFile.test_01.in.bam" ftype="bam"/>
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50 <param name="regex" value='>.*?(chr[^:]):([0-9]+)-([0-9]+)'/>
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52 <output name="dbn_output_file">
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53 <assert_contents>
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54 <has_line_matching expression="&gt;chr1:10-21 x unknown-01 \(aligned reads .*?: 20\)"/>
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55 <has_line line="GGGGAAACCCC"/>
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56 <has_line line="((((...))))&#009;((.((.)).))&#009;-2.5"/>
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57 <has_line line="((.((.)).))&#009;(((((.)))))&#009;-3.5"/>
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59 <has_line_matching expression="&gt;chr1:25-36 x unknown-01 \(aligned reads.*?: 1\)"/>
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60 <has_line line="AAAAAAAAAAA"/>
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61
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62 <has_line_matching expression="&gt;chr1:45-56 x unknown-01 \(aligned reads .*?: 2\)"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67
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68 <help><![CDATA[
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69 This is an utility of the segmentation-fold package
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70 ]]></help>
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72 <expand macro="citations" />
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73 </tool>