Mercurial > repos > bgruening > hicup_digester
comparison hicup_macros.xml @ 3:f6f324d0bb27 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16
author | bgruening |
---|---|
date | Thu, 09 Nov 2017 11:15:47 -0500 |
parents | f220157fbd22 |
children | a2f3a4129052 |
comparison
equal
deleted
inserted
replaced
2:f220157fbd22 | 3:f6f324d0bb27 |
---|---|
12 <stdio> | 12 <stdio> |
13 <exit_code range="1:" /> | 13 <exit_code range="1:" /> |
14 </stdio> | 14 </stdio> |
15 </xml> | 15 </xml> |
16 <xml name="citation_hicup"> | 16 <xml name="citation_hicup"> |
17 <citations> | 17 <citations> |
18 <citation type="doi">10.12688/f1000research.7334.1</citation> | 18 <citation type="doi">10.12688/f1000research.7334.1</citation> |
19 </citations> | 19 </citations> |
20 </xml> | 20 </xml> |
21 <xml name="reference_genome_macro"> | 21 <xml name="reference_genome_macro"> |
22 <conditional name="reference_genome"> | 22 <conditional name="reference_genome"> |
23 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> | 23 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> |
24 <option value="indexed">Use a built-in genome index</option> | 24 <option value="indexed">Use a built-in genome index</option> |
25 <option value="history">Use a genome from the history and build index</option> | 25 <option value="history">Use a genome from the history and build index</option> |
26 </param> | 26 </param> |
27 <when value="indexed"> | 27 <when value="indexed"> |
28 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | 28 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
29 <options from_data_table="bowtie2_indices"> | 29 <options from_data_table="bowtie2_indexes"> |
30 <filter type="sort_by" column="2"/> | 30 <filter type="sort_by" column="2"/> |
31 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | 31 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
32 </options> | 32 </options> |
33 </param> | 33 </param> |
34 </when> | 34 </when> |
60 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" /> | 60 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" /> |
61 <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" /> | 61 <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" /> |
62 <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" /> | 62 <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" /> |
63 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" /> | 63 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" /> |
64 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" /> | 64 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" /> |
65 | |
66 </xml> | 65 </xml> |
67 <xml name="input_files"> | 66 <xml name="input_files"> |
68 <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> | 67 <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> |
69 <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> | 68 <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> |
70 </xml> | 69 </xml> |