Mercurial > repos > bgruening > deeptools
comparison deepTools_macros.xml @ 17:32bb3debd588 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 06 Dec 2013 11:28:08 -0500 |
| parents | 351cd1f8791b |
| children | 449f962a8007 |
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| 16:d0667be9cb0c | 17:32bb3debd588 |
|---|---|
| 25 | 25 |
| 26 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" | 26 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" |
| 27 label ="Include zeros" | 27 label ="Include zeros" |
| 28 help ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." /> | 28 help ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." /> |
| 29 | 29 |
| 30 <param name="zMin" type="integer" value="" label="Minimum value for the heatmap intensities" | 30 <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" |
| 31 help="If not specified the value is set automatically."/> | 31 help="If not specified the value is set automatically."/> |
| 32 | 32 |
| 33 <param name="zMax" type="integer" value="" label="Maximum value for the heatmap intensities" | 33 <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" |
| 34 help="If not specified the value is set automatically."/> | 34 help="If not specified the value is set automatically."/> |
| 35 | 35 |
| 36 <expand macro="colormap" /> | 36 <expand macro="colormap" /> |
| 37 </when> | 37 </when> |
| 38 </conditional> | 38 </conditional> |
| 41 <macro name="requirements"> | 41 <macro name="requirements"> |
| 42 <requirements> | 42 <requirements> |
| 43 <requirement type="package" >samtools</requirement> | 43 <requirement type="package" >samtools</requirement> |
| 44 <requirement type="package" >deepTools</requirement> | 44 <requirement type="package" >deepTools</requirement> |
| 45 <requirement type="package" >ucsc_tools</requirement> | 45 <requirement type="package" >ucsc_tools</requirement> |
| 46 <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement> | 46 <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement> |
| 47 <requirement type="package" version="0.1">ucsc_tools</requirement> | 47 <requirement type="package" version="0.1">ucsc_tools</requirement> |
| 48 <requirement type="package" version="1.7.1">numpy</requirement> | 48 <requirement type="package" version="1.7.1">numpy</requirement> |
| 49 <requirement type="package" version="0.7.7">pysam</requirement> | 49 <requirement type="package" version="0.7.7">pysam</requirement> |
| 50 <requirement type="package" version="0.1.19">samtools</requirement> | 50 <requirement type="package" version="0.1.19">samtools</requirement> |
| 51 <requirement type="package" version="12-2013">bx-python</requirement> | |
| 51 <yield /> | 52 <yield /> |
| 52 </requirements> | 53 </requirements> |
| 53 </macro> | 54 </macro> |
| 54 | 55 |
| 55 <token name="@REFERENCES@"> | 56 <token name="@REFERENCES@"> |
| 102 <option value="cached">locally cached</option> | 103 <option value="cached">locally cached</option> |
| 103 <option value="history">in your history</option> | 104 <option value="history">in your history</option> |
| 104 </param> | 105 </param> |
| 105 <when value="cached"> | 106 <when value="cached"> |
| 106 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | 107 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 107 <options from_data_table="deepTools_seqs" /> | 108 <options from_data_table="deepTools_seqs"> |
| 109 <filter type="sort_by" column="1" /> | |
| 110 <validator type="no_options" message="No indexes are available." /> | |
| 111 </options> | |
| 108 </param> | 112 </param> |
| 109 </when> | 113 </when> |
| 110 <when value="history"> | 114 <when value="history"> |
| 111 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> | 115 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> |
| 112 </when> | 116 </when> |