Mercurial > repos > gbcs-embl-heidelberg > je_markdupes
comparison macros.xml @ 6:7e47f78590cc draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
| author | gbcs-embl-heidelberg |
|---|---|
| date | Fri, 15 Sep 2017 08:18:18 -0400 |
| parents | e2d1b5e1eb11 |
| children | eb38b7dc3810 |
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| 5:e2d1b5e1eb11 | 6:7e47f78590cc |
|---|---|
| 25 #end if | 25 #end if |
| 26 </token> | 26 </token> |
| 27 | 27 |
| 28 <xml name="paired_options"> | 28 <xml name="paired_options"> |
| 29 <when value="paired"> | 29 <when value="paired"> |
| 30 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/> | 30 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #1"/> |
| 31 <param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/> | 31 <param name="input_2" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #2"/> |
| 32 <yield /> | 32 <yield /> |
| 33 <param name="SAME_HEADERS" type="boolean" | 33 <param name="SAME_HEADERS" type="boolean" |
| 34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | 34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" |
| 35 help="Only applies if barcodes are added to the header (option ADD)" | 35 help="Only applies if barcodes are added to the header (option ADD)" |
| 36 truevalue="true" | 36 truevalue="true" |
| 37 falsevalue="false" checked="false"/> | 37 falsevalue="false" checked="false"/> |
| 38 </when> | 38 </when> |
| 39 <when value="paired_collection"> | 39 <when value="paired_collection"> |
| 40 <param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired" | 40 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" |
| 41 label="FASTQ Paired Dataset"/> | 41 label="FASTQ Paired Dataset"/> |
| 42 <yield /> | 42 <yield /> |
| 43 <param name="SAME_HEADERS" type="boolean" | 43 <param name="SAME_HEADERS" type="boolean" |
| 44 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | 44 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" |
| 45 help="Only applies if barcodes are added to the header (option ADD)" | 45 help="Only applies if barcodes are added to the header (option ADD)" |
| 68 <option value="single">Single-end</option> | 68 <option value="single">Single-end</option> |
| 69 <option value="paired">Paired-end</option> | 69 <option value="paired">Paired-end</option> |
| 70 <option value="paired_collection">Paired-end Dataset Collection</option> | 70 <option value="paired_collection">Paired-end Dataset Collection</option> |
| 71 </param> | 71 </param> |
| 72 <when value="single"> | 72 <when value="single"> |
| 73 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> | 73 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/> |
| 74 <param name="I1" type="data" format="fastq,gz" label="First Index File"/> | 74 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/> |
| 75 </when> | 75 </when> |
| 76 <expand macro="paired_options"> | 76 <expand macro="paired_options"> |
| 77 <param name="I1" type="data" format="fastq,gz" label="First Index File"/> | 77 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/> |
| 78 <conditional name="I2_CONDITIONAL"> | 78 <conditional name="I2_CONDITIONAL"> |
| 79 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> | 79 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> |
| 80 <option value="true">Yes</option> | 80 <option value="true">Yes</option> |
| 81 <option value="false" selected="true">No</option> | 81 <option value="false" selected="true">No</option> |
| 82 </param> | 82 </param> |
| 83 <when value="true"> | 83 <when value="true"> |
| 84 <param name="I2" type="data" format="fastq,gz" label="Second Index File"/> | 84 <param name="I2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Second Index File"/> |
| 85 <expand macro="bred_conditional"/> | 85 <expand macro="bred_conditional"/> |
| 86 </when> | 86 </when> |
| 87 <when value="false"/> | 87 <when value="false"/> |
| 88 </conditional> | 88 </conditional> |
| 89 </expand> | 89 </expand> |
| 96 <option value="single">Single-end</option> | 96 <option value="single">Single-end</option> |
| 97 <option value="paired">Paired-end</option> | 97 <option value="paired">Paired-end</option> |
| 98 <option value="paired_collection">Paired-end Dataset Collection</option> | 98 <option value="paired_collection">Paired-end Dataset Collection</option> |
| 99 </param> | 99 </param> |
| 100 <when value="single"> | 100 <when value="single"> |
| 101 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> | 101 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/> |
| 102 </when> | 102 </when> |
| 103 <expand macro="paired_options"> | 103 <expand macro="paired_options"> |
| 104 <yield /> | 104 <yield /> |
| 105 </expand> | 105 </expand> |
| 106 </conditional> | 106 </conditional> |