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planemo upload for repository https://github.com/davebx/bellerophon commit a4601aa6ae17baebc453566301a387d80bd5c3d5
author iuc
date Mon, 04 Sep 2023 07:31:57 +0000
parents 25ca5d73aedf
children
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1 <tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>chimeric reads from Arima Genomics</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement>
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9 <requirement type="package" version="1.12">samtools</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #if $forward.is_of_type("sam"):
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13 #set $forward_input = 'forward_input.sam'
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14 ln -s '${forward}' '$forward_input' &&
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15 #else:
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16 #set $forward_input = 'forward_input.bam'
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17 ln -s '${forward}' '$forward_input' &&
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18 #end if
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19 #if $reverse.is_of_type("sam"):
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20 #set $reverse_input = 'reverse_input.sam'
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21 ln -s '${reverse}' '$reverse_input' &&
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22 #else:
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23 #set $reverse_input = 'reverse_input.bam'
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24 ln -s '${reverse}' '$reverse_input' &&
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25 #end if
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26 bellerophon
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27 --forward $forward_input
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28 --reverse $reverse_input
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29 --quality $quality
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30 --output 'merged_out.bam'
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31 --threads \${GALAXY_SLOTS:-1}
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32 && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads"
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37 help="This is usually the forward reads in your experiment." />
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38 <param argument="--reverse" type="data" format="qname_sorted.bam,sam" label="Second set of reads"
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39 help="This is usually the reverse reads in your experiment." />
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40 <param argument="--quality" type="integer" value="20" label="Minimum mapping quality"/>
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41 </inputs>
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42 <outputs>
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43 <data name="outfile" format="bam"/>
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44 </outputs>
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45 <tests>
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46 <test expect_num_outputs="1">
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47 <param name="forward" value="forward.bam" ftype="qname_sorted.bam" />
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48 <param name="reverse" value="reverse.bam" ftype="qname_sorted.bam" />
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49 <param name="quality" value="20" />
1
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50 <!-- since the tool expects qname_sorted.bam but the bam files are actually coordinate sorted
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51 galaxy sorts them automatically (https://github.com/galaxyproject/galaxy/blob/bfbc537b58e5b00d1e00c37396dbf42a3bd98c5c/lib/galaxy/datatypes/binary.py#L437)
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52 this adds a PG line -->
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53 <output name="outfile" file="merged-out.bam" ftype="bam" lines_diff="2" />
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54 </test>
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55 <test expect_num_outputs="1">
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56 <param name="forward" value="forward.sam" ftype="sam" />
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57 <param name="reverse" value="reverse.sam" ftype="sam" />
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58 <param name="quality" value="12" />
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59 <output name="outfile" file="merged-sam.bam" ftype="bam"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. This is usually needed when dealing with data from Arima Genomics.
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64 ]]></help>
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65 <citations>
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66 <citation type="doi">10.1038/s41586-021-03451-0</citation>
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67 </citations>
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68 </tool>