Mercurial > repos > iuc > stacks2_procrad
annotate stacks_procrad.xml @ 5:b4bab607eb05 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
| author | iuc |
|---|---|
| date | Thu, 14 Apr 2022 09:31:20 +0000 |
| parents | bd5ff77e2036 |
| children |
| rev | line source |
|---|---|
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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changeset
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1 <tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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2 <description>the Stacks demultiplexing script</description> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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3 <macros> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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5 <import>macros_process.xml</import> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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6 </macros> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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7 <expand macro="requirements"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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8 <expand macro="version_cmd"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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9 <command detect_errors="aggressive"><![CDATA[ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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10 @FASTQ_INPUT_FUNCTIONS@ |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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11 |
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5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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diff
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12 #if $input_type.barcode_encoding != '' |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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13 python '$__tool_directory__'/check_bcfile.py '$input_type.barcode' && |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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14 #end if |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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15 mkdir stacks_inputs stacks_outputs && |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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16 |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
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17 #if $output_log |
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ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
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18 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && |
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ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
changeset
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19 #end if |
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ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
diff
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20 |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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21 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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22 $link_command |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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23 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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24 process_radtags |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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25 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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26 @PROCESS_IOOPTIONS@ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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27 @PROCESS_FILTER@ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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28 @COMMON_ADVANCED@ |
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9993234400f1
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 @RESCUE_BARCODE@ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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30 @PROCESS_ADAPTER@ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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31 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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32 ## -E not implemented in Galaxy defaults to phred33 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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33 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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34 ## Restriction enzyme options |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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35 #if str($options_enzyme.enzyme) != '': |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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36 -e $options_enzyme.enzyme |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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37 #end if |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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38 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='': |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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39 --renz_2 $options_enzyme.enzyme2 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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40 #end if |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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41 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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42 ## advanced options not shared between shortreads and radtags |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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43 $options_advanced.bestrad |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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44 $options_advanced.disable_rad_check |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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45 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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46 ## Output options |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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47 ## --merge not implemented in Galaxy |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
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48 |
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0
9993234400f1
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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49 @PROCESS_FASTQ_POSTPROC@ |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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50 ]]></command> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
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51 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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52 <inputs> |
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5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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53 <conditional name="input_type"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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54 <param name="input_type_select" type="select" label="Single-end or paired-end reads"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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55 <option value="single" selected="True">Single-end files</option> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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56 <option value="paired">Paired-end files</option> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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57 </param> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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58 <when value="single"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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59 <param name="fqinputs" argument="-f" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Singles-end reads"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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60 <expand macro="barcode_selector"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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61 <expand macro="barcode_encoding_single" type="Barcode"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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62 </expand> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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63 </when> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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64 <when value="paired"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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65 <param name="fqinputs" type="data_collection" collection_type="list:paired" label="Paired-end reads" format="fastqsanger,fastqsanger.gz"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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66 <expand macro="barcode_selector"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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67 <expand macro="barcode_encoding_pair" type="Barcode"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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68 </expand> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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69 </when> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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70 </conditional> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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71 <conditional name="options_enzyme"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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72 <param name="options_enzyme_selector" type="select" label="Number of enzymes"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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73 <option value="1">One</option> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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74 <option value="2">Two</option> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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75 </param> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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76 <when value="1"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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77 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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78 <expand macro="enzymes"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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79 </param> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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80 </when> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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81 <when value="2"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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82 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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83 <expand macro="enzymes"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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84 </param> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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85 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" > |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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86 <expand macro="enzymes"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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87 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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88 </when> |
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9993234400f1
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89 </conditional> |
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9993234400f1
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90 |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 <section name="options_advanced" title="advanced options" expanded="False"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 <expand macro="common_advanced"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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93 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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94 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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95 <expand macro="rescue_barcode"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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96 <expand macro="process_adapter"/> |
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9993234400f1
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97 </section> |
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98 |
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9993234400f1
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99 <expand macro="process_filter"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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100 <expand macro="process_output_types"/> |
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9993234400f1
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101 <expand macro="in_log"/> |
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9993234400f1
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102 </inputs> |
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103 |
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104 <outputs> |
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105 <expand macro="out_log"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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106 <expand macro="process_outputs"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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107 <collection name="processed" type="list" label="${tool.name} on ${on_string} Processed reads"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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108 <filter>input_type['input_type_select'] == "single"</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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109 <filter>input_type['barcode_encoding'] == ""</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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110 <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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111 </collection> |
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112 <collection name="processed_paired" type="list:paired" label="${tool.name} on ${on_string} Processed reads"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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113 <filter>input_type['input_type_select'] == "paired"</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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114 <filter>input_type['barcode_encoding'] == ""</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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115 <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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116 </collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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117 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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118 <filter>input_type['input_type_select'] == "single"</filter> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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119 <filter>input_type['barcode_encoding'] != ""</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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120 <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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121 </collection> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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122 <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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123 <filter>input_type['input_type_select'] == "paired"</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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124 <filter>input_type['barcode_encoding'] != ""</filter> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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125 <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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126 </collection> |
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127 </expand> |
|
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128 </outputs> |
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129 <tests> |
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130 <!-- 01 single single ended input, no filtering (hence no capturing) + log --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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131 <test expect_num_outputs="2"> |
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132 <param name="input_type|input_type_select" value="single"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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133 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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134 <param name="input_type|barcode_encoding" value="--inline_null"/> |
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5
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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135 <param name="input_type|barcode" value="procrad/barcodes"/> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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136 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
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9993234400f1
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137 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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138 <param name="add_log" value="yes"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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139 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> |
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9993234400f1
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140 <output_collection name="demultiplexed" count="40"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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141 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" compare="contains"/> |
|
0
9993234400f1
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142 </output_collection> |
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143 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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144 <!-- 02 multiple (zipped) single end input (misusing R2 as add single end read file), |
|
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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145 discarding by quality and capturing them --> |
|
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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146 <test expect_num_outputs="3"> |
|
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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147 <param name="input_type|input_type_select" value="single"/> |
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9993234400f1
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148 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> |
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149 <param name="input_type|barcode_encoding" value="--inline_null"/> |
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5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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150 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
9993234400f1
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151 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
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9993234400f1
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152 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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153 <param name="filter_cond|filter_select" value="yes"/> |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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154 <param name="filter_cond|discard" value="-q"/> |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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155 <param name="filter_cond|sliding" value="0.1"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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156 <param name="filter_cond|score" value="11"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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157 <param name="filter_cond|remove" value="-c"/> |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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158 <param name="capture" value="-D"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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159 <param name="outype" value="gzfastq"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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160 <param name="add_log" value="yes"/> |
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ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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161 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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162 <assert_command> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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163 <has_text text="-q"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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164 <has_text text="-w 0.1"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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165 <has_text text="-s 11"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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166 <has_text text="-c"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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167 <has_text text="-D"/> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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168 </assert_command> |
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169 <output_collection name="demultiplexed" count="40"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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170 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
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9993234400f1
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171 </output_collection> |
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172 <output_collection name="discarded" count="2"> |
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5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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173 <element name="R1"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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174 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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175 <has_size value="1101516" delta="200"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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176 <has_text text="@lane1_fakedata0_11 1:N:0:"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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177 </assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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178 </element> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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179 <element name="R2"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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180 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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181 <has_size value="1613724" delta="200"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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182 <has_text text="@lane1_fakedata0_0 1:N:0:"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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183 </assert_contents> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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184 </element> |
|
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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185 </output_collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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186 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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187 <!-- 03 paired input, no quality but length filter, gzfasta output --> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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188 <test expect_num_outputs="4"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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189 <param name="input_type|input_type_select" value="paired"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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190 <param name="input_type|fqinputs"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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191 <collection type="list:paired"> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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192 <element name="reads"> |
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9993234400f1
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193 <collection type="paired"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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194 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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195 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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196 </collection> |
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197 </element> |
|
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198 </collection> |
|
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199 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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200 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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201 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
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9993234400f1
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202 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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203 <param name="filter_cond|filter_select" value="no"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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204 <param name="filter_cond|len_limit" value="50"/> |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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205 <param name="capture" value="-D"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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206 <param name="outype" value="gzfasta"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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207 <param name="add_log" value="yes"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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208 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> |
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209 <assert_command> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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210 <has_text text="--len_limit 50"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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211 </assert_command> |
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212 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
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9993234400f1
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213 <element name="PopA_01"> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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214 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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215 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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216 </element> |
|
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217 </output_collection> |
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218 <output_collection name="remaining" type="list:paired" count="40"> |
|
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219 <element name="PopA_01"> |
|
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220 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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221 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa.gz" ftype="fasta.gz"/> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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222 </element> |
|
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223 </output_collection> |
|
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224 <output_collection name="discarded_paired" type="list:paired" count="1"> |
|
9993234400f1
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225 <element name="reads"> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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226 <element name="forward"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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227 <assert_contents> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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228 <has_size value="609382" delta="200"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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229 <has_text text=">lane1_fakedata0_11 1:N:0:"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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230 </assert_contents> |
|
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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231 </element> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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232 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> |
|
9993234400f1
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233 </element> |
|
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234 </output_collection> |
|
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235 </test> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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236 <!-- 04 paired input (gzipped) + advanced options + two enzymes, fasta output --> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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237 <test expect_num_outputs="3"> |
|
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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238 <param name="input_type|input_type_select" value="paired"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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239 <param name="input_type|fqinputs"> |
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9993234400f1
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iuc
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240 <collection type="list:paired"> |
|
9993234400f1
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iuc
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241 <element name="reads"> |
|
9993234400f1
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242 <collection type="paired"> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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243 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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244 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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245 </collection> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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246 </element> |
|
9993234400f1
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iuc
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247 </collection> |
|
9993234400f1
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248 </param> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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249 <param name="input_type|barcode" value="procrad/barcodes"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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250 <param name="options_enzyme|options_enzyme_selector" value="2"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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251 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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252 <param name="options_enzyme|enzyme2" value="ecoRI"/> |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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253 <param name="options_advanced|truncate" value="70"/> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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254 <param name="options_advanced|rescue_cond|rescue" value="-r"/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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255 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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256 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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257 <param name="options_advanced|bestrad" value="--bestrad"/> |
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1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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258 <param name="options_advanced|retain_header" value="--retain_header"/> |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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259 <param name="options_advanced|disable_rad_check" value="--disable_rad_check"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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260 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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261 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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262 <param name="options_advanced|adapter_mm" value="2"/> |
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0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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263 <param name="outype" value="fasta"/> |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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264 <assert_command> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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265 <has_text text="-e ecoRI"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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266 <has_text text="--renz_2 ecoRI"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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267 <has_text text="-t 70"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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268 <has_text text="-r"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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269 <has_text text="--bestrad"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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270 <has_text text="--retain_header"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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271 <has_text text="--disable_rad_check"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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272 <has_text text="--barcode_dist_1 2"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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273 <has_text text="--barcode_dist_2 2"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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274 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"/> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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275 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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276 <has_text text="--adapter_mm 2"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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277 </assert_command> |
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iuc
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278 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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279 <element name="PopA_01"> |
|
9993234400f1
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iuc
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280 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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281 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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282 </element> |
|
9993234400f1
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iuc
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283 </output_collection> |
|
9993234400f1
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iuc
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284 <output_collection name="remaining" type="list:paired" count="40"> |
|
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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285 <element name="PopA_01"> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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286 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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287 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta"/> |
|
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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288 </element> |
|
9993234400f1
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289 </output_collection> |
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9993234400f1
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290 </test> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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291 <!-- 05 test invalid barcode file --> |
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2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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292 <test expect_failure="true"> |
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bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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293 <param name="input_type|input_type_select" value="single"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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294 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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295 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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296 <param name="input_type|barcode" value="procrad/barcodes-duplicate"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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297 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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298 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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299 <param name="add_log" value="yes"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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300 </test> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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301 <!-- 06 test invalid barcode file --> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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302 <test expect_failure="true"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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303 <param name="input_type|input_type_select" value="single"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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304 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1_01.fq,procrad/R1_02.fq,procrad/R1_03.fq,procrad/R1_04.fq"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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305 <param name="input_type|barcode_encoding" value="--inline_null"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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306 <param name="input_type|barcode" value="procrad/barcodes-duplicate2"/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
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307 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
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308 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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309 <param name="add_log" value="yes"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
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310 </test> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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311 <!-- 07 test no provided barcode file single--> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
312 <test expect_num_outputs="3"> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
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313 <param name="input_type|input_type_select" value="single"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
314 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
315 <param name="input_type|barcode_encoding" value=""/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
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|
316 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
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|
317 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
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318 <param name="add_log" value="yes"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
319 <param name="capture" value="-D"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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320 <output name="output_log"> |
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b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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changeset
|
321 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
322 <has_text text="Barcode Not Found"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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changeset
|
323 <has_text text="Retained Reads"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
324 <has_n_lines n="10"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
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|
325 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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|
326 </output> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
327 <output_collection name="processed" count="1"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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changeset
|
328 <element name="R1"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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changeset
|
329 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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changeset
|
330 <has_size value="20"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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|
331 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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|
332 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
333 </output_collection> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
334 <output_collection name="discarded" count="1"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
335 <element name="R1"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
336 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
337 <has_size value="1613724" delta="200"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
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|
338 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
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|
339 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
340 </output_collection> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
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|
341 </test> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
342 <!-- 08 test no provided barcode file paired --> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
343 <test expect_num_outputs="3"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
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|
344 <param name="input_type|input_type_select" value="paired"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
345 <param name="input_type|fqinputs"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
346 <collection type="list:paired"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
347 <element name="reads"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
348 <collection type="paired"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
349 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
350 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
351 </collection> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
352 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
353 </collection> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
354 </param> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
355 <param name="input_type|barcode_encoding" value=""/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
356 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
|
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
357 <param name="options_enzyme|enzyme" value="ecoRI"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
358 <param name="outype" value="gzfasta"/> |
|
2
bd5ff77e2036
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents:
1
diff
changeset
|
359 <param name="add_log" value="yes"/> |
|
5
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
360 <output name="output_log" file="procrad/process_radtags_paired_no_barcode.out" lines_diff="4"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
361 <output_collection name="processed_paired" type="list:paired" count="2"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
362 <element name="reads_R1_0"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
363 <element name="forward"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
364 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
365 <has_size value="20"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
366 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
367 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
368 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
369 <element name="reads_R2_0"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
370 <element name="reverse"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
371 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
372 <has_size value="20"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
373 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
374 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
375 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
376 </output_collection> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
377 <output_collection name="remaining" type="list:paired" count="2"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
378 <element name="reads_R1_0"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
379 <element name="forward"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
380 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
381 <has_size value="20"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
382 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
383 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
384 </element> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
385 <element name="reads_R2_0"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
386 <element name="reverse"> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
387 <assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
388 <has_size value="17607" delta="100"/> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
changeset
|
389 </assert_contents> |
|
b4bab607eb05
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
parents:
2
diff
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|
390 </element> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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391 </element> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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392 </output_collection> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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393 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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394 </tests> |
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395 <help> |
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396 <![CDATA[ |
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397 .. class:: infomark |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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398 |
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399 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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400 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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401 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but the threshold and window size can be adjusted. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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402 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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403 The process_radtags program can: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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404 |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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405 - handle data that is barcoded, either inline or using an index, or unbarcoded. |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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406 - use combinatorial barcodes. |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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407 - check and correct for a restriction enzyme cutsite for single or double-digested data. |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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408 - filter adapter sequence while allowing for sequencing error in the adapter pattern. |
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9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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409 - process individual files or whole directories of files. |
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9993234400f1
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410 - directly read gzipped data |
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411 - filter reads based on Illumina's Chastity filter |
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412 |
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413 **Help** |
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414 |
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415 Input files: |
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416 |
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417 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list) |
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418 |
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419 - Barcode File |
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420 |
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9993234400f1
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421 The barcode file is a very simple format: |
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422 |
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9993234400f1
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423 ======= =========== |
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9993234400f1
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424 Barcode Sample name |
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425 ======= =========== |
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9993234400f1
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426 ATGGGG PopA_01 |
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427 GGGTAA PopA_02 |
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428 AGGAAA PopA_03 |
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429 TTTAAG PopA_04 |
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430 GGTGTG PopA_05 |
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431 TGATGT PopA_06 |
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432 ======= =========== |
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433 |
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434 Combinatorial barcodes are specified, one per column, separated by a tab: |
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435 |
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436 ======== ======== =========== |
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9993234400f1
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437 Barcode1 Barcode2 Sample name |
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438 ======== ======== =========== |
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439 CGATA ACGTA PopA_01 |
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440 CGGCG CGTA PopA_02 |
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441 GAAGC CGTA PopA_03 |
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442 GAGAT CGTA PopA_04 |
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443 CGATA AGCA PopA_05 |
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444 CGGCG AGCA PopA_06 |
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445 ======== ======== =========== |
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446 |
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447 The sample name column can be omitted. Then the Barcodes are used for naming the output files. |
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448 |
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449 @STACKS_INFOS@ |
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450 ]]> |
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451 </help> |
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452 <expand macro="citation"/> |
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453 </tool> |