Mercurial > repos > rnateam > blockclust
comparison blockclust.xml @ 5:49b72f1013b3 draft
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| author | rnateam |
|---|---|
| date | Tue, 22 Oct 2013 10:15:09 -0400 |
| parents | 4882bc140680 |
| children | b77328c96ac9 |
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| 4:4882bc140680 | 5:49b72f1013b3 |
|---|---|
| 1 <tool id="blockclust" name="BlockClust" version="0.1"> | 1 <tool id="blockclust" name="BlockClust" version="0.1"> |
| 2 <description>Non-coding RNA clustering from deep sequencing read profiles</description> | 2 <description>Non-coding RNA clustering from deep sequencing read profiles</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.0">blockclust</requirement> | 4 <requirement type="package" version="1.0">blockclust</requirement> |
| 5 <requirement type="package" version="3.0.1">R_3_0_1</requirement> | |
| 6 <requirement type="package" version="0.1.19 ">samtools</requirement> | |
| 7 <requirement type="R-module">ggplot2</requirement> | |
| 8 <requirement type="R-module">ape</requirement> | |
| 5 </requirements> | 9 </requirements> |
| 6 <!--<version_command> -version</version_command>--> | 10 <!--<version_command> -version</version_command>--> |
| 7 <command> | 11 <command> |
| 8 #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH | 12 #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH |
| 9 #if str($mode.operation) == "pre": | 13 #if str($mode.operation) == "pre": |
| 59 <option value="mm10">Mouse (mm10)</option> | 63 <option value="mm10">Mouse (mm10)</option> |
| 60 <option value="dm3">Fly (dm3)</option> | 64 <option value="dm3">Fly (dm3)</option> |
| 61 </param> | 65 </param> |
| 62 </when> | 66 </when> |
| 63 <when value="post"> | 67 <when value="post"> |
| 68 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" /> | |
| 64 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" /> | 69 <param name="clusters_bed" type="data" format="bed" label="BED file containing clusters (output of BlockClust)" /> |
| 65 <param name="cmsearch_out" type="data" format="tabular" label="Output of cmsearch tool" /> | |
| 66 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" /> | 70 <param name="sim_tab_in" type="data" format="tabular" label="Pairwise similarities file" /> |
| 67 </when> | 71 </when> |
| 68 </conditional> | 72 </conditional> |
| 69 </inputs> | 73 </inputs> |
| 70 | 74 |
| 71 <outputs> | 75 <outputs> |
| 72 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> | 76 <data format="bed" name="tags_bed" label="BlockClust: BAM to BED on ${on_string}"> |
| 73 <filter> mode["operation"]=="pre"</filter> | 77 <filter> mode["operation"]=="pre"</filter> |
| 74 </data> | 78 </data> |
| 75 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}"> | 79 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > |
| 76 <filter> mode["operation"]=="clust"</filter> | 80 <filter> mode["operation"]=="clust"</filter> |
| 77 </data> | 81 </data> |
| 78 <data format="pdf" name="hclust_plot" label="BlockClust: Hierarchical clustering plot on ${on_string}" > | 82 <data format="bed" name="clusters" label="BlockClust: Clustering BED on ${on_string}"> |
| 79 <filter> mode["operation"]=="clust"</filter> | 83 <filter> mode["operation"]=="clust"</filter> |
| 80 </data> | 84 </data> |
| 81 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> | 85 <data format="tabular" name="sim_tab_out" label="BlockClust: Pairwise similarities on ${on_string}"> |
| 82 <filter> mode["operation"]=="clust"</filter> | 86 <filter> mode["operation"]=="clust"</filter> |
| 83 </data> | 87 </data> |