Mercurial > repos > thanhlv > bin3c

annotate mkmap.xml @ 2:3dc88c0973db draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 3fa036c8cd4aff74e10ced32e0fce0aa1c2819ac-dirty
author thanhlv
date Thu, 03 Oct 2019 05:12:23 -0400
parents 15d48ce4e275
children a8600e2b39b2
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eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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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>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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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 bin3C mkmap
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10 $clobber
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11 --max-image $max_image
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12 --min-extent $min_extent
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-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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14 --min-signal $min_signal
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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15 $eta
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16 #if bin_size != 0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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17 --bin-size $bin_size
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18 #end if
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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19 #if min_insert != 0
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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20 --min-insert $min_insert
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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21 #end if
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22 --min-mapq $min_mapq
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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23 --strong $strong
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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24 #if neb_name != ""
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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25 --enzyme $neb_name
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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26 #end if
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27 $ref $bam out
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28 ]]></command>
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29
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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30 <inputs>
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31 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
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32 <param name="bam" type="data" format="bam" label="Input bam file in query order" />
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33 <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" label="Clobber existing files" />
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34 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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35 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
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36 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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37 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
eb31dd5dc3ed planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 0c7c0f6a955950df029477a0532268bf2b30d269-dirty
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38 <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" />
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39 <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" />
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40 <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" />
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41 <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" />
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42 <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" />
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43 <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
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44 multiple enzymes" />
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45 </inputs>
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46
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47 <outputs>
2
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48 <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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49 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>
0
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57
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58 Documentation can be found at `<https://github.com/cerebis/bin3C>`_.
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59
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60 ]]></help>
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61 <expand macro="citations" />
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62 </tool>