Mercurial > repos > sanbi-uwc > shapeit_phase

annotate shapeit_phase.xml @ 16:1a00583b6b2c draft

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planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
author sanbi-uwc
date Tue, 18 Sep 2018 08:48:52 -0400
parents 201d098d6d67
children 1f460ad509b6
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16
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
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1 <tool id="shapeit_phase" name="shapeit_phase" version="0.15.0">
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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2 <description>genomic data with or without reference panel</description>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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3 <requirements>
4
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sanbi-uwc
parents: 3
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4 <requirement type="package" version="2.r837">shapeit</requirement>
0
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sanbi-uwc
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5 </requirements>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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6 <stdio>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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7 <exit_code range="1:" />
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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8 </stdio>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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9
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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10 <command><![CDATA[
13
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sanbi-uwc
parents: 12
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11 #if str($input_files.input_type_select) == 'plink_bed_bim_fam_list':
11
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sanbi-uwc
parents: 10
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12 ln -s '${input_files.plink_bed_etc_list[0]}' input.plink_bed &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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13 ln -s '${input_files.plink_bed_etc_list[1]}' input.plink_bim &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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14 ln -s '${input_files.plink_bed_etc_list[2]}' input.plink_fam &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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15 echo "BED file" &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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16 ls -l input.plink_bed &&
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sanbi-uwc
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17 echo "BIM file" &&
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sanbi-uwc
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18 head -2 input.plink_bim &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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19 echo "FAM file" &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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20 head -2 input.plink_fam &&
f25ff17454f4 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 10
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21 PART=`head -1 input.plink_bim | cut -f1` &&
9
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22 echo "Working on PART: \$PART" &&
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sanbi-uwc
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23 #else
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24 PART=''
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 12
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25 #end if
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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26 #if str($use_ref_panel.use_ref_panel_select) == "use_ref_panel_yes" and str($use_ref_panel.ref_panel_from_table.ref_panel_from_table_select) == "ref_panel_from_table_yes":
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 12
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27 REF_DIR='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.path}' &&
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
parents: 12
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28 REF_PREFIX='${use_ref_panel.ref_panel_from_table.ref_from_table.fields.reference_prefix}' &&
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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29 SAMPLE_PREFIX="\$REF_DIR/${use_ref_panel.ref_panel_from_table.ref_from_table.fields.sample_prefix}" &&
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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30 SAMPLE=`ls \$SAMPLE_PREFIX*.sample` &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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31 if [ ! -f "\$SAMPLE" ] ; then
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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32 echo "Failed to find valid sample file at \$SAMPLE" >&2 &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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33 exit 1 ;
0
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34 fi &&
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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35 HAP="\${REF_DIR}/\${REF_PREFIX}\${PART}.hap.gz" &&
12
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36 if [ ! -f "\$HAP" ] ; then
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sanbi-uwc
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37 echo "Failed to find valid .hap file at \$HAP" >&2 &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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38 exit 1 ;
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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39 fi &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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40 LEGEND="\${REF_DIR}/\${REF_PREFIX}\${PART}.legend.gz" &&
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557cc7904a2b planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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41 if [ ! -f "\$LEGEND" ] ; then
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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42 echo "Failed to find valid .legend file at \$LEGEND" >&2 &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
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43 exit 1 ;
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sanbi-uwc
parents: 4
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44 fi &&
13
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45 #end if
15
201d098d6d67 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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46 #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes" and $use_genetic_map.genetic_map_from_table.genetic_map_from_table_select == "genetic_map_from_table_yes":
13
b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
sanbi-uwc
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47 MAP_DIR='${use_genetic_map.genetic_map_from_table.map_from_table.fields.path}' &&
5
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48 MAP_PREFIX='${use_genetic_map.genetic_map_from_table.map_from_table.fields.map_prefix}' &&
13
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sanbi-uwc
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49 MAP=`ls \${MAP_DIR}/\${MAP_PREFIX}\${PART}_*` &&
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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50 if [ ! -f "\${MAP}" ] ; then
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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51 echo "Failed to find valid map file at \${MAP}" >&2 &&
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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52 exit 1 ;
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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53 fi &&
3
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54 #end if
5
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sanbi-uwc
parents: 4
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55 #if $input_files.input_type_select == "plink_bed_bim_fam_list":
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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56 echo "COLLECTION NAME:" ${input_files.plink_bed_etc_list.name} &&
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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57 #for $dat in $input_files.plink_bed_etc_list:
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b69dadabf671 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
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58 echo Processing NAME '${dat.name}' &&
5
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59 #end for
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60 #end if
0
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61
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62 shapeit
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63
16
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sanbi-uwc
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64 #if $check_mode != "":
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
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65 -check
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
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66 #end if
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sanbi-uwc
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67
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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68 #if $input_files.input_type_select == "vcf":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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69 --input-vcf ${input_files.vcf_file}
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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70 #else if $input_files.input_type_select == "plink_ped_map":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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71 --input-ped ${input_files.plink_ped} ${input_files.plink_map}
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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72 #if $input_files.plink_missing_code != "0":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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73 --missing_code $input_files.plink_missing_code
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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74 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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75 #else if $input_files.input_type_select == "plink_bed_bim_fam":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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76 --input-bed ${input_files.plink_bed} ${input_files.plink_bim} ${input_files.plink_fam}
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
77 #else if $input_files.input_type_select == "plink_bed_bim_fam_list":
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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diff changeset
78 --input-bed input.plink_bed input.plink_bim input.plink_fam
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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79 #else if $input_files.inputy_type_select == "oxford_gen_sample":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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80 --input-gen ${input_files.oxford_gen} ${input_files.oxford_sample}
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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81 #if $input_files.oxford_threshold != "0.9":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
82 --input-thr $input_files.oxford_threshold
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
83 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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84 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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85
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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86 #if $use_genetic_map.use_genetic_map_select == "use_genetic_map_yes":
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
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87 #if $use_genetic_map.genetic_map_from_table.genetic_map_from_table_select == "genetic_map_from_table_yes":
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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88 --input-map \$MAP
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
diff changeset
89 #else:
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
90 --input-map $use_genetic_map.genetic_map
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
91 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
92 #else if $use_genetic_map.rho != "0.0004":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
93 --rho $use_genetic_map.rho
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
94 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
95
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
96 #if $use_ref_panel.use_ref_panel_select == "use_ref_panel_yes":
5
ceb05c9e6d0a planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 919e9937cdb568591f89a412e22a1124bbb56f77-dirty
sanbi-uwc
parents: 4
diff changeset
97 #if $use_ref_panel.ref_panel_from_table.ref_panel_from_table_select == "ref_panel_from_table_yes":
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
98 --input-ref \$HAP \$LEGEND \$SAMPLE
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
99 #else
3
4a048227b86f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 6dfd47f8de029246dd63d60f24ed685a13f8a2ff-dirty
sanbi-uwc
parents: 0
diff changeset
100 --input-ref $use_ref_panel.ref_panel_from_table.ref_panel_haps $use_ref_panel.ref_panel_from_table.ref_panel_legend $use_ref_panel.ref_panel_from_table.ref_panel_sample
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
101 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
102 #if $use_ref_panel.disable_mcmc_iterations == "disable_mcmc_iterations_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
103 --no-mcmc
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
104 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
105 #if $use_ref_panel.filter_groups == "exclude_groups":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
106 --exclude-grp $use_ref_panel.filter_groups.exclude_groups_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
107 #else if $use_ref_panel.filter_groups == "include_groups":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
108 --include-grp $use_ref_panel.filter_groups.include_groups_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
109 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
110 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
111
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
112 #if $use_filters.use_filters_select == "use_filters_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
113 #if $use_filters.use_input_from == "use_input_from_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
114 --input-from $input_from
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
115 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
116 #if $use_filters.use_input_to == "use_input_to_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
117 --input-to $input_to
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
118 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
119 #if $use_filters.use_output_from == "use_output_from_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
120 --output-from $output_from
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
121 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
122 #if $use_filters.use_output_to == "use_output_to_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
123 --output-to $output_to
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
124 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
125 #if $use_filters.filter_individuals == "exclude_individuals":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
126 --exclude-ind $use_filters.exclude_inviduals_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
127 #else if $use_filters.filter_individuals == "include_individuals":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
128 --include-ind $use_filters.include_inviduals_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
129 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
130 #if $use_filters.filter_individuals == "exclude_SNPs":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
131 --exclude-snp $use_filters.exclude_SNPs_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
132 #else if $use_filters.filter_SNPs == "include_SNPs":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
133 --include-snp $use_filters.include_SNPs_file
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
134 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
135 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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diff changeset
136
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
137 #if $use_advanced_parameters.use_advanced_parameters_select == "use_advanced_parameters_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
138 #if $use_advanced_parameters.chrX == "chrX_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
139 --chrX
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
140 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
141 #if $use_advanced_parameters.noped == "noped_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
142 --noped
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
143 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
144 #if $use_advanced_parameters.states != "100":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
145 --states $use_advanced_parameters.states
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
146 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
147 #if $use_advanced_parameters.window != "2.0":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
148 --window $use_advanced_parameters.window
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
149 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
150 #if $use_advanced_parameters.model_version1 == "use_v1_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
151 --model-version1
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
152 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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diff changeset
153 #if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_european":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
154 --effective-size 11418
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
155 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_african":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
156 --effective-size 17469
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
157 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_asian":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
158 --effective-size 14269
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
159 #else if $use_advanced_parameters.eff_size.eff_size_select == "eff_size_mixedpop":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
160 --effective-size $use_advanced_parameters.eff_size.eff_size_mixed
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
161 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
162 #if $use_advanced_parameters.burn != "7":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
163 --burn $use_advanced_parameters.burn
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
164 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
165 #if $use_advanced_parameters.prune != "8":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
166 --prune $use_advanced_parameters.prune
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
167 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
168 #if $use_advanced_parameters.main != "20":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
169 --main $use_advanced_parameters.main
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
170 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
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diff changeset
171 #if $use_advanced_parameters.threads != "1":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
172 --threads $use_advanced_parameters.threads
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
173 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
174 #if $use_advanced_parameters.set_rng_seed.set_rng_seed_select == "set_rng_seed_yes":
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
175 --seed $use_advanced_parameters.rng_seed
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
176 #end if
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
177 #end if
16
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
178
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
179 #if $check_mode == "":
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
180 --output-max $out_haps $out_sample
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
181 --output-graph $out_graph
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
182 --output-log $out_log
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
183 #else
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
184 --output-log output
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
185 && mv output.mendel.log $out_log
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
186 && mv output.mendel.snp.strand $out_strand
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187 && mv output.mendel.snp.strand.exclude $out_exclude
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188 #end if
0
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189 ]]></command>
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190
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191 <inputs>
16
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192 <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" />
0
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193 <conditional name="input_files">
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194 <param name="input_type_select" type="select" label="Please specify your input files.">
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195 <option value="vcf" selected="True">VCF Variant Call Format</option>
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196 <option value="plink_ped_map">Plink PED/MAP format</option>
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197 <option value="plink_bed_bim_fam">Plink BED/BIM/FAM format</option>
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198 <option value="plink_bed_bim_fam_list">Plink BED/BIM/FAM format list</option>
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199 <option value="oxford_gen_sample">Oxford GEN/SAMPLE format</option>
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200 </param>
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201 <when value="plink_ped_map">
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202 <param name="plink_ped" type="data" format="txt" label="Specify text genotype file (.ped)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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203 <param name="plink_map" type="data" format="txt" label="Specify SNP map file (.map)"/>
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204 <param name="plink_missing_code" type="text" label="Missing data labeled as" value="0"/>
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205 </when>
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206 <when value="plink_bed_bim_fam">
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207 <param name="plink_bed" type="data" format="binary" label="Specify binary genotype file (.bed)"/>
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208 <param name="plink_bim" type="data" format="txt" label="Specify SNP map file (.bim)"/>
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209 <param name="plink_fam" type="data" format="txt" label="Specify individual information file (.fam)"/>
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210 </when>
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211 <when value="plink_bed_bim_fam_list">
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212 <param name="plink_bed_etc_list" type="data_collection" collection_type="list" label="BED/BIM/FAM files as a collection (list)" />
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213 </when>
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214 <when value="oxford_gen_sample">
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215 <param name="oxford_gen" type="data" format="txt" label="Specify text genotype file (.gen)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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216 <param name="oxford_sample" type="data" format="txt" label="Specify individual information file (.sample)"/>
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217 <param name="oxford_threshold" type="float" label="SNP Probability threshold" value="0.9"/>
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218 </when>
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219 <when value="vcf">
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220 <param name="vcf_file" type="data" format="vcf" label="Specify Variant Call Format file (.vcf)"/>
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221 </when>
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222 </conditional>
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223
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224 <conditional name="use_genetic_map">
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225 <param name="use_genetic_map_select" type="select" label="Do you want to use a genetic map?">
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226 <option value="use_genetic_map_yes" selected="True">Yes</option>
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227 <option value="use_genetic_map_no">No</option>
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228 </param>
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229 <when value="use_genetic_map_yes">
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230 <conditional name="genetic_map_from_table">
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231 <param name="genetic_map_from_table_select" type="select" label="Use built in data?">
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232 <option value="genetic_map_from_table_yes" selected="True">Yes</option>
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233 <option value="genetic_map_from_table_no">No</option>
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234 </param>
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235 <when value="genetic_map_from_table_yes">
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236 <param name="map_from_table" type="select" label="Select reference map">
8
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diff changeset
237 <options from_data_table="shapeit2_ref" />
0
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238 </param>
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239 </when>
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240 <when value="genetic_map_from_table_no">
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241 <param name="genetic_map" type="data" format="txt" label="Genetic map file (.gmap)" />
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242 </when>
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243 </conditional>
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244 </when>
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245 <when value="use_genetic_map_no">
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246 <param name="rho" type="float" value="0.0004" label="Adjust recombination rate (--rho) for human data (0.001)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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247 </when>
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248 </conditional>
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249
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250 <conditional name="use_ref_panel">
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251 <param name="use_ref_panel_select" type="select" label="Do you want to use a reference panel?">
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252 <option value="use_ref_panel_yes">Use a reference panel</option>
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253 <option value="use_ref_panel_no" selected="True">Do not use reference panel</option>
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254 </param>
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255 <when value="use_ref_panel_yes">
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256 <conditional name="ref_panel_from_table">
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257 <param name="ref_panel_from_table_select" type="select" label="Use built in data?">
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258 <option value="ref_panel_from_table_yes" selected="True">Yes</option>
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259 <option value="ref_panel_from_table_no">No</option>
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260 </param>
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261 <when value="ref_panel_from_table_yes">
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262 <param name="ref_from_table" type="select" label="Select reference panel">
8
00788810fe57 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 72b6cb6029a3979b51e796a8c210fcf903cf7b23-dirty
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diff changeset
263 <options from_data_table="shapeit2_ref" />
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
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264 </param>
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265 </when>
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266 <when value="ref_panel_from_table_no">
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267 <param name="ref_panel_haps" type="data" format="data" label="Specify reference haplotypes file (.haps)" />
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268 <param name="ref_panel_legend" type="data" format="data" label="Specify SNP map file (.legend)" />
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269 <param name="ref_panel_sample" type="data" format="data" label="Specify individual information file (.sample)" />
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270 </when>
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271 </conditional>
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272 <conditional name="disable_mcmc_iterations">
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273 <param name="disable_mcmc_iterations_select" type="select" label="Disable MCMC iterations">
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274 <option value="disable_mcmc_iterations_yes">Yes</option>
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275 <option value="disable_mcmc_iterations_no" selected="True">No</option>
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276 </param>
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diff changeset
277 <when value="disable_mcmc_iterations_yes"></when>
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278 <when value="disable_mcmc_iterations_no"></when>
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279 </conditional>
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280
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diff changeset
281 <conditional name="filter_groups">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
282 <param name="filter_groups_select" type="select" label="Do you want to filter groups?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
283 <option value="no_individual_filter" selected="True">No filtering</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
284 <option value="exclude_groups">Exclude list of groups</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
285 <option value="include_groups">Limit list of groups</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
286 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
287 <when value="no_individual_filter"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
288 <when value="exclude_groups">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
289 <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded groups (.exc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
290 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
291 <when value="include_groups">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
292 <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited groups (.inc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
293 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
294 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
295
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
296 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
297 <when value="use_ref_panel_no">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
298 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
299 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
300
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
301 <conditional name="use_advanced_parameters">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
302 <param name="use_advanced_parameters_select" type="select" label="Set parameters">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
303 <option value="use_advanced_parameters_yes">Use advanced parameters</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
304 <option value="use_advanced_parameters_no" selected="True">Use standard parameters</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
305 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
306
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
307 <when value="use_advanced_parameters_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
308 <param name="chrX" type="select" label="Use X chromosomal genotypes?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
309 <option value="chrX_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
310 <option value="chrX_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
311 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
312
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
313 <param name="noped" type="select" label="Discard pedigree/family information?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
314 <option value="noped_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
315 <option value="noped_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
316 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
317
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
318 <param name="states" type="integer" label="Number of conditioning haplotypes used during phasing (--states)" value="100"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
319 <param name="window" type="float" label="Window size [Mb] in which conditioning haplotypes are defined" value="2.0"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
320 <param name="model_version1" type="select" label="Use SHAPEIT v1 graphical model">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
321 <option value="use_v1_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
322 <option value="use_v1_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
323 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
324
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
325 <conditional name="eff_size">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
326 <param name="eff_size_select" type="select" label="Effective population size for phasing">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
327 <option value="eff_size_european">European population (11418)</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
328 <option value="eff_size_african">African population (17469)</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
329 <option value="eff_size_asian">Asian population (14269)</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
330 <option value="eff_size_mixed_option" selected="True">Mixed population</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
331 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
332 <when value="eff_size_european"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
333 <when value="eff_size_african"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
334 <when value="eff_size_asian"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
335 <when value="eff_size_mixed_option">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
336 <param name="eff_size_mixed" type="integer" label="Specify effective population size, depending on proportions [11418,17469]" value="14443"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
337 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
338 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
339
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
340 <param name="burn" type="integer" value="7" label="Number of burn-in iterations to find good starting point"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
341 <param name="prune" type="integer" value="8" label="Number of pruning iterations to find parsimonious graphs"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
342 <param name="main" type="integer" value="20" label="Number of iterations to compute transition probabilities"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
343 <param name="threads" type="integer" value="1" label="Specify number of threads"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
344
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
345 <conditional name="set_rng_seed">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
346 <param name="set_rng_seed_select" type="select" label="Set seed for random number generator (RNG)">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
347 <option value="set_rng_seed_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
348 <option value="set_rng_seed_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
349 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
350 <when value="set_rng_seed_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
351 <param name="rng_seed" type="integer" value="18011981" label="RNG seed" />
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
352 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
353 <when value="set_rng_seed_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
354 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
355 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
356 <when value="use_advanced_parameters_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
357 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
358
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
359 <conditional name="use_filters">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
360 <param name="use_filters_select" type="select" label="Apply filtering">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
361 <option value="use_filters_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
362 <option value="use_filters_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
363 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
364 <when value="use_filters_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
365
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
366 <conditional name="use_input_from">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
367 <param name="use_input_from_select" type="select" label="Only consider genotypes above a position?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
368 <option value="use_input_from_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
369 <option value="use_input_from_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
370 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
371 <when value="use_input_from_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
372 <param name="input_from" type="integer" value="1" label="Set position:"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
373 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
374 <when value="use_input_from_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
375 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
376
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
377 <conditional name="use_input_to">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
378 <param name="use_input_to_select" type="select" label="Only consider genotypes above a position?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
379 <option value="use_input_to_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
380 <option value="use_input_to_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
381 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
382 <when value="use_input_to_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
383 <param name="input_to" type="integer" value="1" label="Set position:"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
384 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
385 <when value="use_input_to_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
386 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
387
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
388 <conditional name="use_output_from">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
389 <param name="use_output_from_select" type="select" label="Only output genotypes above a position?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
390 <option value="use_output_from_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
391 <option value="use_output_from_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
392 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
393 <when value="use_output_from_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
394 <param name="output_from" type="integer" value="1" label="Set position:"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
395 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
396 <when value="use_output_from_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
397 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
398
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
399 <conditional name="use_output_to">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
400 <param name="use_output_to_select" type="select" label="Only output genotypes above a position?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
401 <option value="use_output_to_yes">Yes</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
402 <option value="use_output_to_no" selected="True">No</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
403 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
404 <when value="use_output_to_yes">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
405 <param name="output_to" type="integer" value="1" label="Set position:"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
406 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
407 <when value="use_output_to_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
408 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
409
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
410 <conditional name="filter_individuals">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
411 <param name="filter_individuals_select" type="select" label="Do you want to filter individuals?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
412 <option value="no_individual_filter" selected="True">No filtering</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
413 <option value="exclude_individuals">Exclude list of individuals</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
414 <option value="include_individuals">Limit list of individuals</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
415 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
416 <when value="no_individual_filter"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
417 <when value="exclude_individuals">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
418 <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded individuals (.exc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
419 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
420 <when value="include_individuals">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
421 <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited individuals (.inc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
422 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
423 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
424
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
425 <conditional name="filter_SNPs">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
426 <param name="filter_SNPs_select" type="select" label="Do you want to filter SNPs?">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
427 <option value="no_individual_filter" selected="True">No filtering</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
428 <option value="exclude_SNPs">Exclude list of SNPs</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
429 <option value="include_SNPs">Limit list of SNPs</option>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
430 </param>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
431 <when value="no_individual_filter"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
432 <when value="exclude_SNPs">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
433 <param name="exclude_inviduals_file" type="data" format="txt" label="Specify file with excluded SNPs (.exc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
434 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
435 <when value="include_SNPs">
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
436 <param name="include_inviduals_file" type="data" format="txt" label="Specify file with limited SNPs (.inc)"/>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
437 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
438 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
439 </when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
440 <when value="use_filters_no"></when>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
441 </conditional>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
442
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
443 </inputs>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
444 <outputs>
16
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
445 <data name="out_haps" format="tabular" label="${tool.name} on ${on_string} haplotypes (.haps)">
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
446 <filter>not check_mode</filter>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
447 </data>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
448 <data name="out_sample" format="tabular" label="${tool.name} on ${on_string} additional information (.sample)">
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
449 <filter>not check_mode</filter>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
450 </data>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
451 <data name="out_graph" format="txt" label="${tool.name} on ${on_string} haplotype graphs (.hgraph)">
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
452 <filter>not check_mode</filter>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
453 </data>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
454 <data name="out_strand" format="tabular" label="${tool.name} on ${on_string} problematic SNP report (.strand)">
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
455 <filter>check_mode</filter>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
456 </data>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
457 <data name="out_exclude" format="txt" label="${tool.name} on ${on_string} problematic SNPs to exclude (.exclude)">
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
458 <filter>check_mode</filter>
1a00583b6b2c planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty
sanbi-uwc
parents: 15
diff changeset
459 </data>
3
4a048227b86f planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 6dfd47f8de029246dd63d60f24ed685a13f8a2ff-dirty
sanbi-uwc
parents: 0
diff changeset
460 <data name="out_log" format="txt" label="${tool.name} on ${on_string} logfile (.log)"/>
0
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
461 </outputs>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
462 <help><![CDATA[
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
463 TODO: Fill in help.
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
464 ]]></help>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
465 <citations>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
466 <citation type="doi">10.1038/nmeth.1785</citation>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
467 </citations>
97363f287de1 planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 77798d7797f07f1f94f5cecd39195bed15987b56
sanbi-uwc
parents:
diff changeset
468 </tool>