Mercurial > repos > galaxy-australia > purge_haplotigs
annotate purge_haplotigs_cov.xml @ 0:af9c15ba501f draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
author | galaxy-australia |
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date | Wed, 20 Apr 2022 06:46:59 +0000 |
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af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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1 <tool id="purge_haplotigs_cov" name="Purge Haplotigs Cov" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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2 <description>Generate a coverage statistic</description> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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3 <xrefs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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4 <xref type='bio.tools'>purgehaplotigs</xref> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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5 </xrefs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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6 <macros> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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7 <import>macros.xml</import> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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8 </macros> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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9 <expand macro="requirements" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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10 <expand macro="stdio" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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11 <expand macro="version_command" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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12 <command><![CDATA[ |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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13 purge_haplotigs cov |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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14 #if $options.j: |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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15 -j '$options.j' |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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16 #end if |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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17 #if $options.s: |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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18 -s '$options.s' |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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19 #end if |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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20 -i $genomecov |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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21 -l $low_cutoff |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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22 -m $mid_cutoff |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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23 -h $high_cutoff |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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24 cp coverage_stats.csv '$output_statistic' |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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25 2>&1 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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26 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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27 ]]></command> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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28 <inputs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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29 <param name="genomecov" type="data" format="tabular" label="Coverage file" help="Coverage file"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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30 <param name="low_cutoff" type="integer" value="10" label="read depth low cutoff" help="obtain from the histogram"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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31 <param name="mid_cutoff" type="integer" value="20" label="read depth high cutoff" help="Coverage file"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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32 <param name="high_cutoff" type="integer" value="30" label="read depth mid cutoff" help="The low point between the haploid and diploid peaks"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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33 <section name="options" title="Options" expanded="False"> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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34 <param argument="-j" type="integer" value="80" label="Auto-assign contig as j (junk)"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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35 <param argument="-s" type="integer" value="80" label="Auto-assign contig as s (suspected haplogit)"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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36 </section> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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37 </inputs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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38 <outputs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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39 <data name="output_statistic" format="csv" label="${tool.name} on ${on_string}: Coverage Statistic" from_work_dir="coverage_stats.csv"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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40 </outputs> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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41 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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42 <tests> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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43 <test> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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44 <!-- #1 test with common parameters --> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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45 <param name="genomecov" value="aligned.bam.gencov" ftype="tabular"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
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46 <param name="low_cutoff" value="10" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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47 <param name="mid_cutoff" value="20" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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48 <param name="high_cutoff" value="30" /> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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49 <output name="output_statistic" file="coverage_stats.csv" ftype="csv"/> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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50 </test> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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51 </tests> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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52 <help><![CDATA[ |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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53 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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54 .. class:: infomark |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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55 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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56 **What it does** |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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57 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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58 Analyze the coverage on a contig by contig basis. |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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59 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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60 **Input** |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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61 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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62 - input file: a genemecov output file (tabular format) that was produced from purge_haplotigs hist. |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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63 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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64 **Parameters** |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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65 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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66 - l : The read depth low cutoff (use the histogram to eyeball these cutoffs) |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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67 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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68 - m : The low point between the haploid and diploid peaks |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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69 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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70 - h : The read depth high cutoff |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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71 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
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72 - junk : Auto-assign contig as "j" (junk) if this percentage or greater of the contig is low/high coverage (DEFAULT = 80, > 100 = don't junk anything) |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
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73 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
74 - suspect : Auto-assign contig as "s" (suspected haplotig) if this percentage or less of the contig is diploid level of coverage (DEFAULT = 80) |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
75 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
76 **Output** |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
77 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
78 - coverage_stats.csv |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
79 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
80 .. class:: infomark |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
81 |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
82 **References** |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
83 ]]></help> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
84 <citations> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
85 <citation type="doi">DOI: 10.1186/s12859-018-2485-7</citation> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
86 </citations> |
af9c15ba501f
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
galaxy-australia
parents:
diff
changeset
|
87 </tool> |