Mercurial > repos > artbio > bamparse
annotate bamparse.xml @ 1:ae9ea0488850 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 9aec415b3fcc66bf3ed2aad43fd70b57bfe2fb18
| author | artbio |
|---|---|
| date | Sun, 15 Oct 2017 19:14:29 -0400 |
| parents | 2a1a2bc6ae8b |
| children | 8ea06787c08a |
| rev | line source |
|---|---|
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1
ae9ea0488850
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 9aec415b3fcc66bf3ed2aad43fd70b57bfe2fb18
artbio
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1 <tool id="bamparse" name="Count alignments" version="2.0.1"> |
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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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2 <description>in a BAM file</description> |
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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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changeset
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3 <requirements> |
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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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4 <requirement type="package" version="1.1.2">bowtie</requirement> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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5 <requirement type="package" version="1.11.2">numpy</requirement> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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6 <requirement type="package" version="0.11.2.1">pysam</requirement> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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7 </requirements> |
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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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8 <stdio> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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9 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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10 </stdio> |
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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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11 <command detect_errors="exit_code"><![CDATA[ |
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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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12 mkdir outputdir && |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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13 #for $file in $input_list |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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14 samtools index '$file' && |
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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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15 #end for |
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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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16 python $__tool_directory__/bamparse.py |
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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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17 --alignments |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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18 #for $file in $input_list |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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19 '$file' |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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20 #end for |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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21 --labels |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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22 #for $file in $input_list |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
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changeset
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23 '$file.element_identifier' |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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24 #end for |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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25 --polarity '$polarity' |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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26 --number '$output_option' |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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27 ]]></command> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
diff
changeset
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28 <inputs> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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29 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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30 <param name="polarity" type="select" label="how to count sense and antisense reads"> |
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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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changeset
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31 <option value="both">count both sense and antisense reads</option> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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32 <option value="sense">count only sense reads</option> |
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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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33 <option value="antisense">count only antisense reads</option> |
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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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34 </param> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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35 <param name="output_option" type="select" display="radio" label="Select the number of files for results" |
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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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36 help="Results can be returned either as a single multi-column table or in separate two-column |
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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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37 datasets (useful for DESeq subsequent analysis)"> |
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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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38 <option value="unique">A multi-column table</option> |
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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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39 <option value="multiple">One separate two-columns dataset per input bam alignment</option> |
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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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40 </param> |
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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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41 </inputs> |
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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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42 <outputs> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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43 <data name="output" format="tabular" label="Counts"> |
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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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44 <discover_datasets pattern="(?P<designation>.*)\.tabular" ext="tabular" visible="true" assign_primary_output="true" directory="outputdir"/> |
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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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45 </data> |
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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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46 </outputs> |
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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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47 <help> |
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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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48 |
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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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49 **What it does** |
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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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50 |
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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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51 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or |
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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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52 several BAM alignments. |
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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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53 |
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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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54 Sense, antisense or both sense and antisense alignments can be counted |
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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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55 |
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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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56 The library labels in the returned count table are taken from the input bam datasets |
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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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57 names in the Galaxy history. |
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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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58 </help> |
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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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59 <tests> |
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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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60 <test> |
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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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61 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" /> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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62 <param name="polarity" value="both" /> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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63 <param name="output_option" value="unique" /> |
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2a1a2bc6ae8b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
artbio
parents:
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changeset
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64 <output name="output" ftype="tabular" file="table.tabular" /> |
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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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65 </test> |
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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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66 <test> |
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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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67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="tabular" /> |
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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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68 <param name="polarity" value="both" /> |
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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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69 <param name="output_option" value="multiple" /> |
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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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70 <output name="output" ftype="tabular" file="table0.tabular"> |
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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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71 <discovered_dataset designation="table1" ftype="tabular" file="table1.tabular" /> |
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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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72 </output> |
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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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73 </test> |
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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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74 </tests> |
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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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75 </tool> |