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annotate bamparse.xml @ 0:2a1a2bc6ae8b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
author artbio
date Fri, 13 Oct 2017 02:59:36 -0400
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2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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1 <tool id="bamparse" name="Count alignments" version="2.0.0">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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2 <description>in a BAM file</description>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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3 <requirements>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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4 <requirement type="package" version="1.1.2">bowtie</requirement>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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5 <requirement type="package" version="1.11.2">numpy</requirement>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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6 <requirement type="package" version="0.11.2.1">pysam</requirement>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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7 </requirements>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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10 </stdio>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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11 <command detect_errors="exit_code"><![CDATA[
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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12 mkdir outputdir &&
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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13 #for $file in $input_list
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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14 samtools index '$file' &&
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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15 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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16 python $__tool_directory__/bamparse.py
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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17 --alignments
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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18 #for $file in $input_list
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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19 '$file'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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20 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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21 --labels
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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22 #for $file in $input_list
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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23 '$file.element_identifier'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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24 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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25 --polarity '$polarity'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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26 --number '$output_option'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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27 ]]></command>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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28 <inputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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29 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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30 <param name="polarity" type="select" label="how to count sense and antisense reads">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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31 <option value="both">count both sense and antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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32 <option value="sense">count only sense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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33 <option value="antisense">count only antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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34 </param>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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35 <param name="output_option" type="select" display="radio" label="Select the number of files for results"
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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36 help="Results can be returned either as a single multi-column table or in separate two-column
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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37 datasets (useful for DESeq subsequent analysis)">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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38 <option value="unique">A multi-column table</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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39 <option value="multiple">One separate two-columns dataset per input bam alignment</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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40 </param>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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41 </inputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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42 <outputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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43 <data name="output" format="tabular" label="Counts">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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44 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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45 </data>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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46 </outputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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47 <help>
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48
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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49 **What it does**
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50
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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51 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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52 several BAM alignments.
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53
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54 Sense, antisense or both sense and antisense alignments can be counted
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55
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56 The library labels in the returned count table are taken from the input bam datasets
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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57 names in the Galaxy history.
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58 </help>
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59 <tests>
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60 <test>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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61 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" />
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62 <param name="polarity" value="both" />
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63 <param name="output_option" value="unique" />
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64 <output name="output" ftype="tabular" file="table.tabular" />
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65 </test>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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66 <test>
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67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" />
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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68 <param name="polarity" value="both" />
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69 <param name="output_option" value="multiple" />
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70 <output name="output" ftype="tabular" file="table0.tabular">
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71 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" />
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72 </output>
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73 </test>
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74 </tests>
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75 </tool>