Mercurial > repos > bgruening > hicup_mapper

comparison hicup_macros.xml @ 3:f396b479c2f2 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16
author bgruening
date Thu, 09 Nov 2017 11:16:29 -0500
parents 320a2d826a00
children 99dd0efa992b
comparison
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2:320a2d826a00 3:f396b479c2f2
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>