Mercurial > repos > iuc > polypolish
annotate polypolish.xml @ 0:aaa868913641 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
author | iuc |
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date | Thu, 22 Sep 2022 07:51:48 +0000 |
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children | bd2a15dbcea1 |
rev | line source |
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0
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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1 <tool id="polypolish" name="Polypolish" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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2 <description> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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3 Short-read polishing of long-read bacterial genome assemblies |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
4 </description> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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5 <macros> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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6 <import>macro.xml</import> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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7 </macros> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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8 <expand macro='xrefs'/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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9 <expand macro="requirements" /> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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10 <expand macro="version_command" /> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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11 <command detect_errors="aggressive"><![CDATA[ |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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12 ln -s '$input.fasta_file' input_data && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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13 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
14 For single SAM |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
15 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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16 #if $input.sam_data_type.sam_selector == 'single' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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17 #if $input.sam_data_type.single_sam.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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18 samtools view -h $input.sam_data_type.single_sam > input_sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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19 #elif $input.sam_data_type.single_sam.ext == 'sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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20 ln -s $input.sam_data_type.single_sam input_sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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21 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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22 polypolish input_data input_sam > '$polished_fasta' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
23 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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24 For paired SAM |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
25 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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26 #elif $input.sam_data_type.sam_selector == 'paired' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
|
27 #if $input.sam_data_type.R1_sam.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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28 samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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29 #elif $input.sam_data_type.R1_sam.ext == 'sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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30 ln -s '$input.sam_data_type.R1_sam' sample_R1.sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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31 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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32 #if $input.sam_data_type.R2_sam.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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33 samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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34 #elif $input.sam_data_type.R2_sam.ext == 'sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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35 ln -s '$input.sam_data_type.R2_sam' sample_R2.sam && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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36 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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37 #if $input.sam_data_type.insert_filter.filter_select == 'filter' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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38 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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39 --high '$input.sam_data_type.insert_filter.high' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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40 --in1 sample_R1.sam |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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41 --in2 sample_R2.sam |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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42 --out1 'filtered_1.sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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43 --out2 'filtered_2.sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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44 polypolish input_data 'filtered_1.sam' 'filtered_2.sam' > $polished_fasta |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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45 #else |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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46 polypolish input_data sample_R1.sam sample_R2.sam > $polished_fasta |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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47 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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48 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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49 For multiple single-end SAM |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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50 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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51 #elif $input.sam_data_type.sam_selector == 'multiple_single' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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52 mkdir single_collection && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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53 #for $value, $single_sam in enumerate($input.sam_data_type.single_collection): |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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54 #if $single_sam.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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55 samtools view -h $single_sam > 'single_collection/$(single_sam.element_identifier).sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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56 #elif $single_sam.ext == 'sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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57 ln -s $single_sam 'single_collection/$(single_sam.element_identifier).$(single_sam.ext)' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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58 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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59 #end for |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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60 polypolish input_data single_collection/*.sam > '$polished_fasta' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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61 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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62 For multiple paired-end SAM |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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63 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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64 #elif $input.sam_data_type.sam_selector == "multiple_paired" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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65 mkdir paired_collection && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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66 #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection): |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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67 #if $paired_sam.forward.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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68 samtools view -h $paired_sam.forward > 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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69 #else |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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70 ln -s '$paired_sam.forward' 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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71 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
changeset
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72 #if $paired_sam.reverse.ext == 'unsorted.bam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
parents:
diff
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73 samtools view -h $paired_sam.reverse > 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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74 #else |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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75 ln -s '$paired_sam.reverse' 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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76 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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77 #if $input.sam_data_type.insert_filter.filter_select == 'filter' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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78 polypolish_insert_filter.py --low '$input.sam_data_type.insert_filter.low' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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79 --high '$input.sam_data_type.insert_filter.high' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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80 --in1 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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81 --in2 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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82 --out1 'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier)_filtered.sam' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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83 --out2 'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier)_filtered.sam' && |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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84 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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85 #end for |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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86 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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87 Filtering option |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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88 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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89 #if $input.sam_data_type.insert_filter.filter_select == 'filter' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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90 polypolish input_data paired_collection/*_filtered.sam > '$polished_fasta' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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91 #else |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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92 polypolish input_data paired_collection/*.sam > '$polished_fasta' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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93 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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94 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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95 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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96 For debug file output |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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97 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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98 #if $options.debug == 'true' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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99 --debug $debug_file |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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100 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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101 #*====================================== |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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102 For LOGFILE OUTPUT |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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103 ======================================*# |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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104 #if $options.keep_logfile == 'true' |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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105 | tee '$logfile' |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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106 #end if |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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107 ]]> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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108 </command> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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109 <inputs> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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110 <section name="input" title="Input sequences" expanded="True"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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111 <param name="fasta_file" type="data" format="fasta" label="Select a draft genome for polishing" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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112 help="Fasta sequence to be cleaned using short-reads data"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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113 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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114 <param name="sam_selector" type="select" label="Select aligned data to polish" help="Choose number of aligned sam/bam files. Need aligned file with all possible locations in aligner option"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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115 <option value="single">Single SAM/BAM file</option> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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116 <option value="paired">Paired SAM/BAM files</option> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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117 <option value="multiple_single">Multiple single SAM/BAM files</option> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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118 <option value="multiple_paired">Multiple paired SAM/BAM files</option> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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119 </param> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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120 <when value="single"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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121 <param name="single_sam" type="data" format="sam,unsorted.bam" label="Select a SAM/BAM file" help="Specify dataset with only one SAM/BAM file"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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122 </when> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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123 <when value="paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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124 <param name="R1_sam" type="data" format="sam,unsorted.bam" label="Select forward SAM/BAM file" help="Specify the forward SAM/BAM files"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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125 <param name="R2_sam" type="data" format="sam,unsorted.bam" label="Select reverse SAM/BAM file" help="Specify the reverse SAM/BAM files"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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126 <expand macro="filter_option"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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127 </when> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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128 <when value="multiple_single"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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129 <param name="single_collection" format="sam,unsorted.bam" type="data_collection" collection_type="list" label="Single-end collection" help="Specify a list of single-end dataset"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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130 </when> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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131 <when value="multiple_paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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132 <param name="paired_collection" format="sam,unsorted.bam" type="data_collection" collection_type="list:paired" label="Single-end collection" help="Specify a list of single-end dataset"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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133 <expand macro="filter_option"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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134 </when> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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135 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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136 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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137 <section name="options" title="Options" expanded="False"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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138 <param name="min_depth" argument="--min_depth" type="integer" min="0" value="5" label="Minimal depth" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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139 help="A base must occur at least this many times in the pileup to be considered valid [default: 5]"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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140 <param name="fraction_invalid" argument="--fraction_invalid" type="float" min="0" value="0.2" max="1" label="Minimal invalid fraction" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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141 help="A base must make up less than this fraction of the read depth to be considered invalid [default: 0.2]"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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142 <param name="max_errors" argument="--max_errors" type="integer" min="0" value="10" label="Number of mismatch/indels to ignore alignments" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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143 help="Ignore alignments with more than this many mismatches and indels [default: 10]"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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144 <param name="fraction_valid" argument="--fraction_valid" type="float" min="0" value="0.5" max="1" label="Minimal valid fraction" |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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145 help="A base must make up at least this fraction of the read depth to be considered valid [default: 0.5"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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146 <param name="keep_logfile" type="boolean" truevalue="true" falsevalue="false" label="Keep log file"/> |
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147 <param name="debug" argument="--debug" type="boolean" truevalue="true" falsevalue="false" label="Keep per base information file"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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148 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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149 </inputs> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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150 <outputs> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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151 <data name="polished_fasta" format="fasta" label="${tool.name} on ${on_string}: polished fasta"/> |
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152 <data name="debug_file" format="tabular" label="${tool.name} on ${on_string}: Per base informations"> |
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153 <filter> options['debug'] == True </filter> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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154 </data> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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155 <data name="logfile" format="txt" from_work_dir="output" label="${tool.name} on ${on_string}: log report"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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156 <filter> options['keep_logfile'] == True </filter> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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157 </data> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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158 </outputs> |
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159 <tests> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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160 <!-- Test_1 with default values and single SAM --> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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161 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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162 <section name="input"> |
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163 <param name="fasta_file" value="contigs.fa"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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164 <conditional name="sam_data_type"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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165 <param name="sam_selector" value="single"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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166 <param name="single_sam" value="aligned_test_file/alignement_R1.sam"/> |
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167 </conditional> |
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168 </section> |
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169 <output name="polished_fasta" value="polished.fasta"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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170 </test> |
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171 <!-- Test_2 with default values and paired SAM --> |
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172 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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173 <section name="input"> |
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174 <param name="fasta_file" value="contigs.fa"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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175 <conditional name="sam_data_type"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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176 <param name="sam_selector" value="paired"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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177 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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178 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> |
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179 </conditional> |
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180 </section> |
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181 <section name="options"> |
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182 <param name="debug" value="true"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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183 <param name="keep_logfile" value="false"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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184 </section> |
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185 <output name="polished_fasta" value="polished.fasta"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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186 <output name="debug_file" value="debug_file_test_2.tsv"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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187 </test> |
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188 <!-- Test_3 with default values and single-end multiple SAM --> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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189 <test expect_num_outputs="2"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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190 <section name="input"> |
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191 <param name="fasta_file" value="contigs.fa"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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192 <conditional name="sam_data_type"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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193 <param name="sam_selector" value="multiple_single"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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194 <param name="single_collection"> |
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195 <collection type="list"> |
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196 <element name="R1_sam" value="aligned_test_file/alignement_R1.sam" ftype="sam"/> |
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197 <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.sam" ftype="sam"/> |
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198 <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.sam" ftype="sam"/> |
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199 </collection> |
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200 </param> |
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201 </conditional> |
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202 </section> |
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203 <section name="options"> |
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204 <param name="debug" value="false"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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205 <param name="keep_logfile" value="true"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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206 </section> |
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207 <output name="polished_fasta" value="polished.fasta"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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208 <output name="logfile" value="logfile_test_3.log" lines_diff="15"/> |
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209 </test> |
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210 <!-- Test_4 with default values and paired collection SAM --> |
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211 <test expect_num_outputs="1"> |
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212 <section name="input"> |
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213 <param name="fasta_file" value="contigs.fa"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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214 <conditional name="sam_data_type"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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215 <param name="sam_selector" value="multiple_paired"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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216 <param name="paired_collection"> |
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217 <collection type="list:paired"> |
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218 <element name="paired_1"> |
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219 <collection type="paired"> |
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220 <element name="forward" value="aligned_test_file/alignement_R1.sam" ftype="sam"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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221 <element name="reverse" value="aligned_test_file/alignement_R2.sam" ftype="sam"/> |
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222 </collection> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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223 </element> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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224 <element name="paired_2"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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225 <collection type="paired"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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226 <element name="forward" value="aligned_test_file/alignement_R1_bis.sam" ftype="sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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227 <element name="reverse" value="aligned_test_file/alignement_R2_bis.sam" ftype="sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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228 </collection> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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229 </element> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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230 <element name="paired_3"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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231 <collection type="paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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232 <element name="forward" value="aligned_test_file/alignement_R1_ter.sam" ftype="sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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233 <element name="reverse" value="aligned_test_file/alignement_R2_ter.sam" ftype="sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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234 </collection> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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235 </element> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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236 </collection> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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237 </param> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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238 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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239 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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240 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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241 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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242 <!-- Test_5 paired-end without filtering and whitout log file --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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243 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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244 <section name="input"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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245 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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246 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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247 <param name="sam_selector" value="paired"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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248 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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249 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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250 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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251 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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252 <section name="options"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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253 <conditional name="insert_filter"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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254 <param name="filter_select" value="non_filter"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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255 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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256 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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257 <param name="keep_logfile" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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258 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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259 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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260 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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261 <!-- Test_6 paired-end with filter, user defined values and whitout log file --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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262 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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263 <section name="input"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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264 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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265 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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266 <param name="sam_selector" value="paired"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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267 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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268 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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269 <conditional name="insert_filter"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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270 <param name="filter_select" value="filter"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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271 <param name="low" value="1"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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272 <param name="high" value="98.7"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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273 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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274 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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275 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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276 <section name="options"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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277 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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278 <param name="keep_logfile" value="false"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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279 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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280 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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281 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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282 <!-- Test_7 paired-end with all customized filters --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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283 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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284 <section name="input"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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285 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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286 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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287 <param name="sam_selector" value="paired"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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288 <param name="R1_sam" value="aligned_test_file/alignement_R1.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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289 <param name="R2_sam" value="aligned_test_file/alignement_R2.sam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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290 <conditional name="insert_filter"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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291 <param name="filter_select" value="filter"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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292 <param name="low" value="1.4"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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293 <param name="high" value="96.6"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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294 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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295 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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296 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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297 <section name="options"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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298 <param name="min_depth" value="10"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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299 <param name="fraction_invalid" value="0.5"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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300 <param name="max_errors" value="8"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
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301 <param name="fraction_valid" value="0.6"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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302 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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303 <param name="keep_logfile" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
304 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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305 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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306 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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307 <!-- Test_8 single with bam input --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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308 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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309 <section name="input"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
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310 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
311 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
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312 <param name="sam_selector" value="single"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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313 <param name="single_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
314 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
315 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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316 <section name="options"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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317 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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318 <param name="keep_logfile" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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319 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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320 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
321 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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322 <!-- Test_9 paired-end with bam input --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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323 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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324 <section name="input"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
325 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
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326 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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327 <param name="sam_selector" value="paired"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
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328 <param name="R1_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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329 <param name="R2_sam" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
330 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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331 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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332 <section name="options"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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333 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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334 <param name="keep_logfile" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
335 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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336 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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337 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
338 <!-- Test_10 single collection with bam input --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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339 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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340 <section name="input"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
341 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
342 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
343 <param name="sam_selector" value="multiple_single"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
344 <param name="single_collection"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
345 <collection type="list"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
346 <element name="R1_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
347 <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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|
348 <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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349 </collection> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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350 </param> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
351 </conditional> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
352 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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353 <section name="options"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
354 <param name="debug" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
355 <param name="keep_logfile" value="false"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
356 </section> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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357 <output name="polished_fasta" value="polished.fasta"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
358 </test> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
359 <!-- Test_11 paired-end with bam input --> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
360 <test expect_num_outputs="1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
361 <section name="input"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
362 <param name="fasta_file" value="contigs.fa"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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diff
changeset
|
363 <conditional name="sam_data_type"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
364 <param name="sam_selector" value="multiple_paired"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
365 <param name="paired_collection"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
366 <collection type="list:paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
367 <element name="paired_1"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
368 <collection type="paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
369 <element name="forward" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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changeset
|
370 <element name="reverse" value="aligned_test_file/alignement_R2.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
371 </collection> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
372 </element> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
373 <element name="paired_2"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
374 <collection type="paired"> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
iuc
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|
375 <element name="forward" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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376 <element name="reverse" value="aligned_test_file/alignement_R2_bis.bam" ftype="unsorted.bam"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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377 </collection> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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378 </element> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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379 <element name="paired_3"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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380 <collection type="paired"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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381 <element name="forward" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/> |
aaa868913641
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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382 <element name="reverse" value="aligned_test_file/alignement_R2_ter.bam" ftype="unsorted.bam"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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383 </collection> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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384 </element> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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385 </collection> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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386 </param> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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387 </conditional> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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388 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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389 <section name="options"> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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390 <param name="debug" value="false"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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391 <param name="keep_logfile" value="false"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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392 </section> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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393 <output name="polished_fasta" value="polished.fasta"/> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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394 </test> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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395 </tests> |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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396 <help><![CDATA[ |
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397 **What it does** |
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398 Polypolish is a tool for polishing genome assemblies with short reads. |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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399 Polypolish uses SAM/BAM files where each read has been aligned to all possible locations (not just a single best location). |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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400 This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. |
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401 |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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402 **Polypolish pipeline steps** |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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403 1. [Optional] Filter aligned reads |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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404 - Exclude some alignments based on their insert size |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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405 - This should reduce the number of excessive alignments, particularly near the edges of repeat sequences, improving Polypolish's ability to fix errors in those regions. |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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406 2. Clean assembly with filtered reads |
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407 |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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408 **Inputs** |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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409 Polypolish need SAM/BAM input format obtain from aligner with option to keep all possible location |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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410 Polypolish take on or more assembly as input fasta. |
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411 It need also raw data reads in single or paired-end SAM/BAM format. |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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412 You can use multiple aligned data to polish the same assembly. |
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413 **WARNING It can only work if multiple location information is available in sam/bam files** |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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414 For example using bwa mem to align raw data before use, you need : |
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415 1. To align each read data independantly (also for paired data) |
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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
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416 2. Set the option "Output all alignments for single-ends or unpaired paired-ends" in Select analysis mode>Set input/output options |
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417 - This allow multiple ailgnemnt output need to use polypolish |
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418 |
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419 |
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420 ]]></help> |
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421 <expand macro="citations"/> |
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422 </tool> |