Mercurial > repos > iuc > stacks2_procrad
annotate stacks_procrad.xml @ 1:ca7aa77c7f57 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author | iuc |
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date | Mon, 30 Sep 2019 14:20:50 -0400 |
parents | 9993234400f1 |
children | bd5ff77e2036 |
rev | line source |
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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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1 <tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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2 <description>the Stacks demultiplexing script</description> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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3 <macros> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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4 <import>macros.xml</import> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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5 <import>macros_process.xml</import> |
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> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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7 <expand macro="requirements"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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8 <expand macro="version_cmd"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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9 <command detect_errors="aggressive"><![CDATA[ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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10 @FASTQ_INPUT_FUNCTIONS@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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11 mkdir stacks_inputs stacks_outputs && |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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12 |
1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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13 #if $output_log |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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14 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
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15 #end if |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
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16 |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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17 #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:
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18 $link_command |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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19 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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20 process_radtags |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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21 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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22 @PROCESS_IOOPTIONS@ |
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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23 @PROCESS_FILTER@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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24 @COMMON_ADVANCED@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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25 @RESCUE_BARCODE@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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26 @PROCESS_ADAPTER@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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27 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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28 ## -E not implemented in Galaxy defaults to phred33 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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29 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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30 ## Restriction enzyme options |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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31 #if str($options_enzyme.enzyme) != '': |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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32 -e $options_enzyme.enzyme |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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33 #end if |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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34 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='': |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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35 --renz_2 $options_enzyme.enzyme2 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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36 #end if |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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37 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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38 ## advanced options not shared between shortreads and radtags |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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39 $options_advanced.bestrad |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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40 $options_advanced.disable_rad_check |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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41 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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42 ## Output options |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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43 ## --merge not implemented in Galaxy |
1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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0
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44 |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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45 @PROCESS_FASTQ_POSTPROC@ |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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46 ]]></command> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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47 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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48 <inputs> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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49 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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50 <conditional name="options_enzyme"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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51 <param name="options_enzyme_selector" type="select" label="Number of enzymes"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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52 <option value="1">One</option> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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53 <option value="2">Two</option> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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54 </param> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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55 <when value="1"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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56 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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57 <expand macro="enzymes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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58 </param> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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59 </when> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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60 <when value="2"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
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61 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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62 <expand macro="enzymes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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63 </param> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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64 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" > |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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65 <expand macro="enzymes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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66 </param> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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67 </when> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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68 </conditional> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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69 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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70 <section name="options_advanced" title="advanced options" expanded="False"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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71 <expand macro="common_advanced"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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72 <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" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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73 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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74 <expand macro="rescue_barcode"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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75 <expand macro="process_adapter"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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76 </section> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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77 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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78 <expand macro="process_filter"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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79 <expand macro="process_output_types"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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80 <expand macro="in_log"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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81 </inputs> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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82 |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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83 <outputs> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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84 <expand macro="out_log"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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85 <expand macro="process_outputs"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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86 </outputs> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
87 <tests> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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88 <!-- single single ended input, no filtering (hence no capturing) + log --> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
89 <test> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
90 <param name="input_type|input_type_select" value="single"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
91 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
92 <param name="input_type|barcode_encoding" value="--inline_null"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
93 <param name="barcode" value="procrad/barcodes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
94 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff
changeset
|
95 <param name="options_enzyme|enzyme" value="ecoRI"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
96 <param name="add_log" value="yes" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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97 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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changeset
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98 <output_collection name="demultiplexed" count="40"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
99 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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100 </output_collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
101 </test> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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102 <!-- multiple (zipped) single end input (misusing R2 as add single end read file), |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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103 discarding by quality and capturing them --> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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104 <test> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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105 <param name="input_type|input_type_select" value="single"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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106 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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107 <param name="input_type|barcode_encoding" value="--inline_null"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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108 <param name="barcode" value="procrad/barcodes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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109 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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110 <param name="options_enzyme|enzyme" value="ecoRI"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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111 <param name="filter_cond|filter_select" value="yes"/> |
1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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112 <param name="filter_cond|discard" value="-q"/> |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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113 <param name="filter_cond|sliding" value="0.1" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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114 <param name="filter_cond|score" value="11" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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115 <param name="filter_cond|remove" value="-c" /> |
1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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116 <param name="capture" value="-D"/> |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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117 <param name="outype" value="gzfastq"/> |
1
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
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118 <param name="add_log" value="yes" /> |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents:
0
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119 <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
iuc
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120 <assert_command> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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121 <has_text text="-q" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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122 <has_text text="-w 0.1" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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123 <has_text text="-s 11" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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124 <has_text text="-c" /> |
1
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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125 <has_text text="-D" /> |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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126 </assert_command> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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127 <output_collection name="demultiplexed" count="40"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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128 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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129 </output_collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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130 <output_collection name="discarded" count="2"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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131 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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132 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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133 </output_collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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134 </test> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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135 <!-- paired input, no quality but length filter, gzfasta output --> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
136 <test> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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137 <param name="input_type|input_type_select" value="paired"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
138 <param name="input_type|fqinputs"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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139 <collection type="list:paired"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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140 <element name="reads"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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141 <collection type="paired"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
142 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
143 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
144 </collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
145 </element> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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146 </collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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147 </param> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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148 <param name="barcode" value="procrad/barcodes"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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149 <param name="options_enzyme|options_enzyme_selector" value="1"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
150 <param name="options_enzyme|enzyme" value="ecoRI"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
151 <param name="filter_cond|filter_select" value="no"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
152 <param name="filter_cond|len_limit" value="50"/> |
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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|
153 <param name="capture" value="-D"/> |
0
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
154 <param name="outype" value="gzfasta"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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155 <param name="add_log" value="yes" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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|
156 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
157 <assert_command> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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158 <has_text text="--len_limit 50" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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|
159 </assert_command> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
160 <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
iuc
parents:
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changeset
|
161 <element name="PopA_01"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
162 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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|
163 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz" /> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
164 </element> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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165 </output_collection> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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|
166 <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
parents:
diff
changeset
|
167 <element name="PopA_01"> |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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changeset
|
168 <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
iuc
parents:
diff
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|
169 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa.gz" ftype="fasta.gz"/> |
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170 </element> |
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171 </output_collection> |
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172 <output_collection name="discarded_paired" type="list:paired" count="1"> |
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173 <element name="reads"> |
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174 <element name="forward" file="procrad/R1.fa.discards" ftype="fasta"/> |
9993234400f1
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175 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/> |
9993234400f1
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176 </element> |
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177 </output_collection> |
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178 </test> |
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179 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output --> |
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180 <test> |
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181 <param name="input_type|input_type_select" value="paired"/> |
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182 <param name="input_type|fqinputs"> |
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183 <collection type="list:paired"> |
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184 <element name="reads"> |
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185 <collection type="paired"> |
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186 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" /> |
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187 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/> |
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188 </collection> |
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189 </element> |
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190 </collection> |
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191 </param> |
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192 <param name="barcode" value="procrad/barcodes"/> |
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193 <param name="options_enzyme|options_enzyme_selector" value="2"/> |
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194 <param name="options_enzyme|enzyme" value="ecoRI"/> |
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195 <param name="options_enzyme|enzyme2" value="ecoRI"/> |
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196 <param name="options_advanced|truncate" value="70" /> |
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197 <param name="options_advanced|rescue_cond|rescue" value="-r"/> |
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198 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> |
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199 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> |
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200 <param name="options_advanced|bestrad" value="--bestrad" /> |
1
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201 <param name="options_advanced|retain_header" value="--retain_header"/> |
0
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202 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> |
1
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203 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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204 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> |
ca7aa77c7f57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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205 <param name="options_advanced|adapter_mm" value="2" /> |
0
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206 <param name="outype" value="fasta"/> |
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207 <assert_command> |
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208 <has_text text="-e ecoRI" /> |
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209 <has_text text="--renz_2 ecoRI" /> |
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210 <has_text text="-t 70" /> |
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211 <has_text text="-r" /> |
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212 <has_text text="--bestrad" /> |
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213 <has_text text="--retain_header" /> |
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214 <has_text text="--disable_rad_check" /> |
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215 <has_text text="--barcode_dist_1 2" /> |
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216 <has_text text="--barcode_dist_2 2" /> |
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217 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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218 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> |
0
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219 <has_text text="--adapter_mm 2" /> |
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220 </assert_command> |
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221 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> |
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222 <element name="PopA_01"> |
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223 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/> |
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224 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/> |
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225 </element> |
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226 </output_collection> |
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227 <output_collection name="remaining" type="list:paired" count="40"> |
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228 <element name="PopA_01"> |
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229 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" /> |
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230 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" /> |
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231 </element> |
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232 </output_collection> |
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233 </test> |
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234 </tests> |
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235 |
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236 <help> |
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237 <![CDATA[ |
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238 .. class:: infomark |
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239 |
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240 **What it does** |
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241 |
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242 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. |
9993234400f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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243 |
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244 The process_radtags program can: |
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245 |
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246 - handle data that is barcoded, either inline or using an index, or unbarcoded. |
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247 - use combinatorial barcodes. |
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248 - check and correct for a restriction enzyme cutsite for single or double-digested data. |
9993234400f1
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249 - filter adapter sequence while allowing for sequencing error in the adapter pattern. |
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250 - process individual files or whole directories of files. |
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251 - directly read gzipped data |
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252 - filter reads based on Illumina's Chastity filter |
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253 |
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254 **Help** |
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255 |
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256 Input files: |
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257 |
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258 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list) |
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259 |
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260 - Barcode File |
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261 |
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262 The barcode file is a very simple format: |
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263 |
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264 ======= =========== |
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265 Barcode Sample name |
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266 ======= =========== |
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267 ATGGGG PopA_01 |
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268 GGGTAA PopA_02 |
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269 AGGAAA PopA_03 |
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270 TTTAAG PopA_04 |
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271 GGTGTG PopA_05 |
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272 TGATGT PopA_06 |
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273 ======= =========== |
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274 |
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275 Combinatorial barcodes are specified, one per column, separated by a tab: |
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276 |
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277 ======== ======== =========== |
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278 Barcode1 Barcode2 Sample name |
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279 ======== ======== =========== |
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280 CGATA ACGTA PopA_01 |
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281 CGGCG CGTA PopA_02 |
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282 GAAGC CGTA PopA_03 |
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283 GAGAT CGTA PopA_04 |
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284 CGATA AGCA PopA_05 |
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285 CGGCG AGCA PopA_06 |
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286 ======== ======== =========== |
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287 |
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288 The sample name column can be omitted. Then the Barcodes are used for naming the output files. |
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289 |
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290 @STACKS_INFOS@ |
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291 ]]> |
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292 </help> |
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293 <expand macro="citation" /> |
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294 </tool> |