Mercurial > repos > iuc > stacks2_tsv2bam
annotate stacks_tsv2bam.xml @ 4:69842dd5aa48 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author | iuc |
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date | Wed, 01 Sep 2021 11:32:48 +0000 |
parents | bf0e43ab0416 |
children | a4b4bd84f69e |
rev | line source |
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0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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2 <description>Sort reads by RAD locus</description> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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3 <macros> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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4 <import>macros.xml</import> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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5 </macros> |
4
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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6 <expand macro="requirements"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
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7 <requirement type="package" version="1.13">samtools</requirement> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
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8 </expand> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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9 <expand macro="version_cmd"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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10 <command detect_errors="aggressive"><![CDATA[ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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11 @FASTQ_INPUT_FUNCTIONS@ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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12 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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13 mkdir stacks_inputs stacks_outputs && |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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14 |
1
8c2617661c49
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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15 #if $output_log |
8c2617661c49
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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16 ln -s '$output_log' stacks_inputs/tsv2bam.log && |
8c2617661c49
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
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17 #end if |
8c2617661c49
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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18 |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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19 @LINK_STACKS_INPUT@ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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20 @LINK_CAT_INPUT@ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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21 @LINK_MATCHES_INPUT@ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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22 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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23 ## link fastq files into stacks_inputs/ |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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24 #set $paired_reads=False |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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25 #for $sample in $input_type.fqinputs: |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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26 #if not $sample: |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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27 #continue |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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28 #end if |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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29 #set $paired_reads=True |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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30 #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2") |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
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31 $link_cmd |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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32 #end for |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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33 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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34 tsv2bam |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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35 -P stacks_inputs |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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36 #if $popmap |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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37 -M '$popmap' |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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38 #else |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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39 #for $sample in $samples |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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40 -s '$sample' |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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41 #end for |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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42 #end if |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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43 #if $paired_reads |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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44 --pe-reads-dir stacks_inputs |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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45 #end if |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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46 -t \${GALAXY_SLOTS:-1} |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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47 ## tsv2bam writes to stdout and creates a log file |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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48 ## - make stdout stderr |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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49 ## - move the additional log file |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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50 2>&1 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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51 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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52 && mv stacks_inputs/*matches.bam stacks_outputs |
4
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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53 |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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54 ## see comment in gstacks |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
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55 && for b in stacks_outputs/*matches.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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56 ]]></command> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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57 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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58 <inputs> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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59 <expand macro="input_stacks_macro"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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60 <expand macro="input_cat_macro"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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61 <expand macro="input_matches_macro"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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62 <!-- TODO add BAM? --> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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63 <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/> |
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bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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64 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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65 <expand macro="in_log"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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66 </inputs> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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67 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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68 <outputs> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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69 <expand macro="out_log"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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70 <expand macro="tsv2bam_outputs_macro"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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71 </outputs> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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72 |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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73 <tests> |
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69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
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74 <!-- test wo paired end data (this is not the default used in denovomap .. which is used for generating the test data therefore we only test if a list of two bams is generated) --> |
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bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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75 <test expect_num_outputs="2"> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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76 <param name="input_cat"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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77 <collection type="list"> |
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bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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78 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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79 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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80 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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81 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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82 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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83 <param name="input_stacks"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
84 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
85 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
86 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
87 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
88 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
89 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
90 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
91 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
92 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
93 <param name="input_matches"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
94 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
95 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
96 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
97 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
98 </param> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
99 <param name="add_log" value="yes"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
100 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/> |
4
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
101 <output_collection name="bams" type="list" count="2"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
102 </test> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
103 <!-- test w popmap, w reverse reads as multiple selection --> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
104 <test expect_num_outputs="2"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
105 <param name="input_cat"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
106 <collection type="list"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
107 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
108 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
109 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
110 </collection> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
111 </param> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
112 <param name="input_stacks"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
113 <collection type="list"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
115 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
116 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
117 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
118 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
119 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
120 </collection> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
121 </param> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
122 <param name="input_matches"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
123 <collection type="list"> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
124 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
125 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
126 </collection> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
127 </param> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
128 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
129 <param name="input_type|input_type_select" value="single"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
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|
130 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
131 <param name="add_log" value="yes"/> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
132 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
69842dd5aa48
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents:
2
diff
changeset
|
133 <output_collection name="bams" type="list" count="2"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
134 </test> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
135 <!-- test w popmap, w reverse reads as multiple selection --> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
136 <test expect_num_outputs="2"> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
137 <param name="input_cat"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
138 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
139 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
140 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
141 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
142 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
143 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
144 <param name="input_stacks"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
145 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
146 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
147 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
148 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
149 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
150 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
151 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
152 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
153 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
154 <param name="input_matches"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
155 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
156 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
157 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
158 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
159 </param> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
160 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
161 <param name="input_type|input_type_select" value="single"/> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
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diff
changeset
|
162 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
163 <param name="add_log" value="yes"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
164 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
165 <output_collection name="bams" type="list" count="2"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
166 </test> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
167 <!-- test w reverse reads as list --> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
168 <test expect_num_outputs="2"> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
169 <param name="input_cat"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
170 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
171 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
172 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
173 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
174 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
175 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
176 <param name="input_stacks"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
177 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
178 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
179 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
180 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
181 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
182 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
183 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
184 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
185 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
186 <param name="input_matches"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
187 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
188 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
189 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
190 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
191 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
192 <param name="input_type|input_type_select" value="paired"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
193 <param name="input_type|fqinputs"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
194 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
195 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
196 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
197 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
198 </param> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
199 <param name="add_log" value="yes"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
200 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
201 <output_collection name="bams" type="list" count="2"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
202 </test> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
203 <!-- test w paired reads as paired dataset list --> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
204 <test expect_num_outputs="2"> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
205 <param name="input_cat"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
206 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
207 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
208 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
209 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
210 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
211 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
212 <param name="input_stacks"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
213 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
214 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
215 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
216 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
217 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
218 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
219 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
220 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
221 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
222 <param name="input_matches"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
223 <collection type="list"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
224 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/> |
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
225 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
226 </collection> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
227 </param> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
228 <param name="input_type|input_type_select" value="paired"/> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
229 <param name="input_type|fqinputs"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
230 <collection type="list:paired"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
231 <element name="PopA_01"> |
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
232 <collection type="paired"> |
2
bf0e43ab0416
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
233 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/> |
0
1b270fc77c81
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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234 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/> |
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235 </collection> |
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236 </element> |
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237 <element name="PopA_02"> |
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238 <collection type="paired"> |
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239 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/> |
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240 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/> |
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241 </collection> |
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242 </element> |
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243 </collection> |
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244 </param> |
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245 <param name="add_log" value="yes"/> |
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246 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output> |
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247 <output_collection name="bams" type="list" count="2"/> |
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248 </test> |
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249 </tests> |
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250 |
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251 <help> |
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252 <![CDATA[ |
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253 .. class:: infomark |
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254 |
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255 **What it does** |
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256 |
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257 The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework |
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258 |
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259 -------- |
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260 |
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261 **Input files** |
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262 |
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263 FASTQ, FASTA |
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264 |
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265 **Output files** |
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266 |
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267 - XXX.tags.tsv file: |
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268 |
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269 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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270 |
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271 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence. |
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272 |
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273 |
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274 - XXX.snps.tsv file: |
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275 |
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276 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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277 |
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278 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one. |
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279 |
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280 |
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281 - XXX.alleles.tsv file: |
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282 |
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283 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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284 |
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285 @STACKS_INFOS@ |
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286 ]]> |
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287 </help> |
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288 <expand macro="citation"/> |
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289 </tool> |