Mercurial > repos > jackcurragh > ribogalaxy_create_ribosome_profile
comparison create_ribosome_profile/create_ribosome_profile.xml @ 5:4d69f7428243 draft
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| author | jackcurragh |
|---|---|
| date | Wed, 18 May 2022 12:02:46 +0000 |
| parents | 49e8fcbaaa72 |
| children | 8f8affaa5eb4 |
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| 4:49e8fcbaaa72 | 5:4d69f7428243 |
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| 10 #else: | 10 #else: |
| 11 ${refGenomeSource.input1_file} none ${input4} ${output1} | 11 ${refGenomeSource.input1_file} none ${input4} ${output1} |
| 12 #end if | 12 #end if |
| 13 </command> | 13 </command> |
| 14 <inputs> | 14 <inputs> |
| 15 <param name="input1" type="data" format="bam" label="BAM file to process"/> | 15 <conditional name="refGenomeSource"> |
| 16 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/> | 16 <param name="input1" type="data" format="bam" label="BAM file to process"/> |
| 17 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> | 17 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/> |
| 18 <option value="builtin">Use a built-in FASTA</option> | 18 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?"> |
| 19 <option value="history">Use one from the history</option> | 19 <option value="builtin">Use a built-in FASTA</option> |
| 20 </param> | 20 <option value="history">Use one from the history</option> |
| 21 <when value="builtin"> | |
| 22 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> | |
| 23 <options from_data_table="builtin_fastas"> | |
| 24 <filter type="sort_by" column="2" /> | |
| 25 <validator type="no_options" message="No built-ins are available" /> | |
| 26 </options> | |
| 27 </param> | 21 </param> |
| 28 </when> | 22 <when value="builtin"> |
| 29 <when value="history"> | 23 <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team"> |
| 30 <param name="input1_file" type="data" format="fasta" label="FASTA File" /> | 24 <options from_data_table="builtin_fastas"> |
| 31 </when> | 25 <filter type="sort_by" column="2" /> |
| 26 <validator type="no_options" message="No built-ins are available" /> | |
| 27 </options> | |
| 28 </param> | |
| 29 </when> | |
| 30 <when value="history"> | |
| 31 <param name="input1_file" type="data" format="fasta" label="FASTA File" /> | |
| 32 </when> | |
| 33 </conditional> | |
| 32 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/> | 34 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/> |
| 33 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase"> | 35 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase"> |
| 34 <option value="offset" selected="true">Use offset approach</option> | 36 <option value="offset" selected="true">Use offset approach</option> |
| 35 <option value="weight">Use weight centered approach</option> | 37 <option value="weight">Use weight centered approach</option> |
| 36 </param> | 38 </param> |