Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
comparison readmap.xml @ 4:dffa22efc6a8 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Mon, 29 Jun 2015 05:54:47 -0400 |
| parents | f6dc63230483 |
| children | 6ee5a6e89aa4 |
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| 3:f6dc63230483 | 4:dffa22efc6a8 |
|---|---|
| 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.2"> | 1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.2"> |
| 2 <description>from sRbowtie aligment</description> | 2 <description>from sRbowtie aligment</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.12.7">bowtie</requirement> | 4 <requirement type="package" version="0.12.7">bowtie</requirement> |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 6 <requirement type="package" version="0.7.7">pysam</requirement> | 5 <requirement type="package" version="0.7.7">pysam</requirement> |
| 7 <requirement type="package" version="2.14">biocbasics</requirement> | 6 <requirement type="package" version="2.14">biocbasics</requirement> |
| 8 <requirement type="package" version="1.9">numpy</requirement> | 7 <requirement type="package" version="1.9">numpy</requirement> |
| 9 </requirements> | 8 </requirements> |
| 10 <command interpreter="python"> | 9 <command interpreter="python"> |
| 55 <option value="indexed">Use a built-in index</option> | 54 <option value="indexed">Use a built-in index</option> |
| 56 <option value="history">Use one from the history</option> | 55 <option value="history">Use one from the history</option> |
| 57 </param> | 56 </param> |
| 58 <when value="indexed"> | 57 <when value="indexed"> |
| 59 <repeat name="series" title="Add alignment files"> | 58 <repeat name="series" title="Add alignment files"> |
| 60 <param name="input" type="data" label="Select multiple alignments to parse"> | 59 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"> |
| 61 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> | 60 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> |
| 62 </param> | 61 </param> |
| 63 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> | 62 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> |
| 64 </repeat> | 63 </repeat> |
| 65 </when> | 64 </when> |
| 66 <when value="history"> | 65 <when value="history"> |
| 67 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> | 66 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" /> |
| 68 <repeat name="series" title="Add alignment files"> | 67 <repeat name="series" title="Add alignment files"> |
| 69 <param name="input" type="data" label="Select multiple alignments to parse"/> | 68 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/> |
| 70 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> | 69 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/> |
| 71 </repeat> | 70 </repeat> |
| 72 </when> | 71 </when> |
| 73 </conditional> | 72 </conditional> |
| 74 <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> | 73 <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/> |