Mercurial > repos > thanhlv > bin3c

annotate mkmap.xml @ 17:1971cfa55ada draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 9f4ab03111185c7e20aaf669586278744713eee4
author thanhlv
date Mon, 21 Oct 2019 05:26:18 -0400
parents cdfc397e7b0f
children 327acdd0663d
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1 <tool id="mkmap" name="mkmap" version="@VERSION@">
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2 <description>Create a new contact map from assembly sequences and Hi-C bam file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 samtools sort -@ \${GALAXY_SLOTS:-1} -o sorted.bam -n $bam &&
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10 bin3C mkmap
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11 --min-extent $min_extent
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12 --min-reflen $min_reflen
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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13 --min-signal $min_signal
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14 #if str($bin_size) != "0":
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15 --bin-size $bin_size
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16 #end if
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17 --min-insert $min_insert
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18 --min-mapq $min_mapq
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19 $eta
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20 --strong $strong
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21 #if str($neb_name) != "":
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22 #for $enzyme in str($neb_name).split(',')
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23 -e $enzyme
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24 #end for
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25 #end if
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26 $ref sorted.bam out
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27 ]]></command>
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29 <inputs>
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30 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
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31 <param name="bam" type="data" format="bam" label="Input bam file in query order" />
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32 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
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33 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
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34 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
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35 <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" />
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36 <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" />
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37 <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" />
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38 <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" />
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39 <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" />
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40 <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
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41 multiple enzymes">
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42 <help><![CDATA[Use , (comma) to separate multiple enzymes e.g enzyme1,enzyme2]]> </help>
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43 </param>
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44 </inputs>
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46 <outputs>
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47 <data name="contact_map" format="tar.gz" label="${tool.name} on ${on_string} Contact map" from_work_dir="out/contact_map.p.gz"/>
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48 <data name="log" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
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49 </outputs>
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51 <tests>
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52 <test>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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57 Documentation can be found at `<https://github.com/cerebis/bin3C>`_.
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58
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59 ]]></help>
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60 <expand macro="citations" />
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61 </tool>