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1 <?xml version="1.0"?>
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2 <tool name="labels" id="bg_labels" version="1.0.5.0">
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3 <description>remapper and annotator of alignments</description>
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4 <requirements>
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5 <requirement type="package" version="1.0.5">labels</requirement>
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6 <requirement type="package" version="0.7.7">pysam</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 pylapels
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17 -c "${chrom_list}"
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18 $alias
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19 $sorted
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20 -p \${GALAXY_SLOTS:-4}
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21 -q
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22 -o $output
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23 $input_mod
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24 $input_bam
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="input_bam" type="data" format="bam" label="BAM file">
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1
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29 <!--validator type="unspecified_build" />
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30 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /-->
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31 </param>
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1
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32 <param name="input_mod" type="data" format="txt" label="MOD file"/>
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0
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33
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34 <param name="alias" optional="true" type="data" format="tabular" label="CSV? file for alias classes of sequence name"/>
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35 <param name="sorted" type="boolean" truevalue="-n" falsevalue=""
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36 label="Sort the output BAM file by read names" help="-n"/>
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37 <param name="chrom_list" type="text" value="all" label="Comma-separated list of chromosomes in the output" help="e.g. 1,2,3 (-c)" />
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38
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39 </inputs>
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40 <outputs>
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41 <data name="output" format="bam" label="${tool.name} on ${on_string}"/>
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42 </outputs>
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43 <tests>
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44
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45 </tests>
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46 <help>
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47 <![CDATA[
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48
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49 **What it does**
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50
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51 A remapper and annotator of in silico (pseudo) genome alignments.
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52
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53 https://code.google.com/p/lapels/
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54
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55 ]]>
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56 </help>
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57 </tool>
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