Mercurial > repos > iuc > bcftools_call

annotate macros.xml @ 1:3b0006e824c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 93465571cf180554c3548338a68fa0f1604985dc
author iuc
date Tue, 05 Apr 2016 13:19:31 -0400
parents dabc1e7ca486
children 0812cba3c4c8
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <macros>
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3 <token name="@VERSION@">1.2</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <!-- This requirement handles also bcftools from BioConda channel => https://github.com/bioconda/bioconda-recipes/tree/60d2ea750430dbe0191f6f8d5639f90fc1223bd9/recipes/bcftools/1.2 -->
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dabc1e7ca486 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 97a064489364118d108b0dd2cfb4d9bc53080837
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7 <requirement type="package" version="1.2">bcftools</requirement>
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8 </requirements>
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9 </xml>
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10 <xml name="version_command">
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11 <version_command><![CDATA[bcftools 2>&1 | grep 'Version:']]></version_command>
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12 </xml>
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13 <xml name="citations">
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14 <citations>
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15 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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16 <yield />
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17 </citations>
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18 </xml>
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19 <xml name="macro_exclude">
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20 <param name="exclude" label="Exclude" help="exclude sites for which the expression is true (see man page for details)" />
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21 </xml>
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22 <xml name="macro_collapse">
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23 <param name="collapse" label="Collapse" type="select" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
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24 <option value="snps">snps</option>
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25 <option value="indels">indels</option>
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26 <option value="both">both</option>
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27 <option value="all">all</option>
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28 <option value="some">some</option>
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29 <option value="none" selected="True">None</option>
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30 </param>
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31 </xml>
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32 <xml name="macro_apply_filters_repeat">
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33 <repeat name="apply_filters_repeat" title="Apply Filters">
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34 <param name="apply_filters" label="Apply Filters" help="require at least one of the listed FILTER strings (e.g. &quot;PASS,.&quot;)" />
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35 </repeat>
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36 </xml>
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37
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38 <token name="@SEC_DEF_REGIONS@">
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39 #if $sec_default.regions_file:
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40 --regions-file "${sec_default.regions_file}"
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41 #end if
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42 </token>
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43 <token name="@SEC_DEF_TARGETS@">
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44 #if $sec_default.targets_file:
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45 --targets-file "${sec_default.targets_file}"
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46 #end if
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47 </token>
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48 <token name="@SEC_DEF_SAMPLES@">
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49 #if $sec_default.samples_file:
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50 --samples-file "${sec_default.samples_file}"
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51 #end if
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52 </token>
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53
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54 <xml name="macro_samples">
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55 <param name="samples_file" label="Samples File" type="data" format="data" optional="True" help="file of samples to include" />
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56 <param name="invert_samples_file" label="Invert Samples" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the sample file selection" />
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57 </xml>
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58 <xml name="macro_targets">
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59 <param name="targets_file" label="Targets File" type="data" format="data" optional="True" help="similar to -R but streams rather than index-jumps" />
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60 <param name="invert_targets_file" label="Invert Targets" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the target file selection" />
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61 </xml>
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62 <xml name="macro_regions">
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63 <param name="regions_file" label="Regions File" type="data" format="data" optional="True" help="restrict to regions listed in a file" />
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64 <param name="invert_regions_file" label="Invert Regions" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by region file selection" />
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65 </xml>
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66 <xml name="macro_select_output_type">
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67 <param name="select_output_type" type="select">
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68 <option value="v" selected="True">uncompressed VCF</option>
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69 <option value="z">compressed VCF</option>
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70 <option value="u">uncompressed BCF</option>
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71 <option value="b">compressed BCF</option>
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72 </param>
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73 </xml>
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74 </macros>