Mercurial > repos > rnateam > dewseq

annotate dewseq.xml @ 0:e1cb2e012307 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
author rnateam
date Thu, 20 Oct 2022 08:18:30 +0000
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e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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1 <tool id="dewseq" name="DEWSeq" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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3 <description>- A sliding window based peak caller for eCLIP/iCLIP data</description>
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4 <requirements>
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5 <requirement type="package" version="3.10">python</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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6 <requirement type="package" version="1.8.0">bioconductor-dewseq</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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7 <requirement type="package" version="2.16">r-rmarkdown</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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8 <requirement type="package" version="2.22.0">bioconductor-biocstyle</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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9 <requirement type="package" version="1.3.2">r-tidyverse</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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10 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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11 <requirement type="package" version="1.22.0">bioconductor-ihw</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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12 <requirement type="package" version="2.7.3">r-magick</requirement>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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13 </requirements>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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15 <command detect_errors="exit_code"><![CDATA[
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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16 python '$__tool_directory__/dewseq_wrapper.py'
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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17 --out ./
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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18 --annot $annot_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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19 --matrix $matrix_file
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20 --info $info_file
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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21 --ds-ms $ds_ms
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22 --ds-mc $ds_mc
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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23 --ds-pvc $ds_pvc
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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24 --ds-lfcc $ds_lfcc
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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25 $ds_use_oc
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26 $ds_disable_ihw
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27 $ds_disable_df
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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28 $ds_use_lrt
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29 --ds-id $ds_id
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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30 --ds-markdown '$__tool_directory__/analyseStudy.Rmd'
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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31 --copy-md
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32
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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33 ]]></command>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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34
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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35 <inputs>
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36 <param name="annot_file" type="data" format="tabular"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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37 label="Windows annotation file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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38 help="Windows annotation table file (output of htseq-clip 'Create sliding windows' Galaxy wrapper)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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39 <param name="matrix_file" type="data" format="tabular"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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40 label="Count table file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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41 help="CLIP-seq samples count table file (output of htseq-clip 'Create count table' Galaxy wrapper)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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42 <param name="info_file" type="data" format="tabular"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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43 label="Sample information table file"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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44 help="CLIP-seq sample information table file (output of htseq-clip 'Create count table' Galaxy wrapper)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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45 <param name="ds_ms" type="integer" value="2"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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46 label="DEWSeq min_sample parameter"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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47 help="Keep only windows where at least min_sample samples have a crosslink site count > min_count (including control samples) (default: 2)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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48 <param name="ds_mc" type="integer" value="2"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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49 label="DEWSeq min_count parameter"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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50 help="Minimum crosslink site count per window per sample (default: 2)"/>
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51 <param name="ds_pvc" type="float" value="0.1"
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52 label="DEWSeq p_value_cutoff parameter"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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53 help="Adjusted p-value threshold for a window to be reported as significant window (default: 0.1)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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54 <param name="ds_lfcc" type="float" value="1.0"
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55 label="DEWSeq lfc_cutoff parameter"
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56 help="Log2 fold change threshold for a window to be reported as significant window (default: 1.0)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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57 <param name="ds_use_oc" label="Use overlapping windows p-value correction?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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58 truevalue="--ds-oc" falsevalue="" checked="False"
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59 help="Choose yes to adjust p-values for overlapping windows, using Bonferroni family-wise error rate correction on overlapping sliding windows"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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60 <param name="ds_disable_ihw" label="Disable IHW?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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61 truevalue="--ds--disable-ihw" falsevalue="" checked="False"
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62 help="Choose yes to disable independent hypothesis weighting (IHW) for multiple testing correction. By default, IHW is used for multiple tesing correction instead of the default method Benjamini Hochberg (BH). The authors recommend using IHW instead of BH for FDR correction"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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63 <param name="ds_disable_df" label="Disable DEWSeq's decide_fit?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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64 truevalue="--ds--disable-df" falsevalue="" checked="False"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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65 help="Choose yes if DEWSeq should not decide on the type of dispersion estimation fit to be used. By default, DEWSeq decides on the dispersion estimation fit type (local or parametric). If this option is enabled, parametric fit will be used instead. By default, DEWSeq fits data using both parametric and local fit types and chooses the best fit of the two (see documentation for details). Typically, this should give better results, but keep in mind that this will also increase the total run time"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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66 <param name="ds_use_lrt" label="Use LRT instead of Wald test?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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67 truevalue="--ds-use-lrt" falsevalue="" checked="False"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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68 help="Choose yes to use likelihood ratio test (LRT) instead of Wald test (see documentation for details). By default, DEWSeq uses Wald test. The authors note that LRT is more accurate than Wald test, but one should keep in mind that LRT is a stringent test in comparison to Wald. So if the RNA-binding protein of interest is a very active binder, it can make sense to enable LRT, otherwise it should be used with caution as one may end up with little or no significant windows at all"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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69 <param name="ds_id" type="text" value="RBP"
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70 label="DEWSeq dataset ID"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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71 help="DEWSeq dataset ID for output HTML report (default: RBP)"/>
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72
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73 <section name="output_options" title="Output options">
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74 <param name="sig_reg_bed_out" label="Output significant regions BED file?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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75 checked="False"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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76 help="Output significant regions BED file. Regions can be made up of single significant windows or merged adjacent significant windows (column 7: mean adjusted p-value of region, column 8: mean log2 fold change of region)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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77 <param name="sig_win_reg_bed_out" label="Output significant windows + regions BED file?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
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78 checked="False"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
79 help="Output significant windows + regions BED file. This outputs both significant regions and if the region is made up of several windows the single significant windows as well (corresponds to output_bed_file in the DEWSeq R markdown script)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
80 <param name="report_html_out" label="Output HTML report file?" type="boolean"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
81 checked="False"
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
82 help="Output HTML report file (corresponds to output_file in the DEWSeq R markdown script)"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
83 </section>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
84
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
85 </inputs>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
86 <outputs>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
87 <data format="csv" name="win_csv_file" label="${tool.name} on ${on_string}: All windows CSV file" from_work_dir="windows.csv"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
88 <data format="csv" name="sig_reg_csv_file" label="${tool.name} on ${on_string}: Significant regions CSV file" from_work_dir="significant_regions.csv"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
89 <data name="sig_reg_bed_file" format="bed" from_work_dir="significant_regions.bed" label="${tool.name} on ${on_string}: Significant regions BED file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
90 <filter>(output_options['sig_reg_bed_out'] is True)</filter>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
91 </data>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
92 <data name="sig_win_reg_bed_file" format="bed" from_work_dir="significant_windows_and_regions.bed" label="${tool.name} on ${on_string}: Significant regions + windows BED file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
93 <filter>(output_options['sig_win_reg_bed_out'] is True)</filter>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
94 </data>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
95 <data name="html_report_file" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: HTML report file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
96 <filter>(output_options['report_html_out'] is True)</filter>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
97 </data>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
98 </outputs>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
99
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
100 <tests>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
101 <test>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
102 <param name="annot_file" value="windows.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
103 <param name="matrix_file" value="Rbp_count_matrix.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
104 <param name="info_file" value="sample_info.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
105 <param name="ds_pvc" value="0.5"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
106 <param name="sig_reg_bed_out" value="True"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
107 <param name="sig_win_reg_bed_out" value="True"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
108 <param name="report_html_out" value="True"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
109 <output name="win_csv_file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
110 <assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
111 <has_n_lines n="673"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
112 <has_n_columns n="22"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
113 </assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
114 </output>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
115 <output name="sig_reg_csv_file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
116 <assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
117 <has_n_lines n="151"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
118 <has_n_columns n="21"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
119 </assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
120 </output>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
121 <output name="sig_reg_bed_file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
122 <assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
123 <has_n_lines n="150"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
124 <has_n_columns n="8"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
125 </assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
126 </output>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
127 <output name="sig_win_reg_bed_file" file="significant_windows_and_regions.bed"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
128 <output name="html_report_file" file="report.html" compare="sim_size"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
129 </test>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
130
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
131 <test>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
132 <param name="annot_file" value="windows.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
133 <param name="matrix_file" value="Rbp_count_matrix.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
134 <param name="info_file" value="sample_info.exp.txt" ftype="tabular"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
135 <param name="ds_pvc" value="0.5"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
136 <param name="ds_use_lrt" value="True"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
137 <output name="win_csv_file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
138 <assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
139 <has_n_lines n="673"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
140 <has_n_columns n="22"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
141 </assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
142 </output>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
143 <output name="sig_reg_csv_file">
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
144 <assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
145 <has_n_lines n="2"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
146 <has_n_columns n="21"/>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
147 </assert_contents>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
148 </output>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
149 </test>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
150
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
151 </tests>
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
152 <help><![CDATA[
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
153
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
154 **Overview**
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
155
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
156 DEWSeq_ is a peak caller for CLIP-seq data, i.e., to identify the RNA binding sites of RNA-binding proteins from CLIP-seq data. It uses a sliding window approach together with DESeq2 for the analysis of differentially enriched binding regions in CLIP-seq (typically eCLIP or iCLIP) sequencing data.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
157 The CLIP-seq data (starting from the mapped reads BAM files) needs to be preprocessed by htseq-clip_ (available on Galaxy as well), which provides the input files for DEWSeq.
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
158
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
159
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
160 **Output files**
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
diff changeset
161
e1cb2e012307 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq commit 71db0e65b3b306904ae2b17ce3de677244aea776"
rnateam
parents:
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162 By default, the wrapper outputs two CSV table files (all windows CSV, significant regions CSV). In addition, BED files including significant regions and windows can be output, as well as an HTML report file (see Output options for details).
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163
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164
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165 *All windows CSV file*:
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166
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167 This file corresponds to the output_windows_file in the DEWSeq R markdown script (see documentation link below for details), and includes all input windows and the corresponding p-values and log2 fold changes.
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168
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169 *Significant regions CSV file*:
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170
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171 This file corresponds to the output_regions_file in the DEWSeq R markdown script (see documentation link below for details), and reports all significant regions, which can also consist of several windows, if two or more adjacent windows are significant.
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172 The window IDs that belong to each region can be found the "unique_ids" column. "regionStartId" is the most upstream window ID in the region.
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173 Mean, maximum, and minimum adjusted p-values and log2 fold changes for each region are also given. An emtpy file is returned if no significant regions were found.
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174
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175
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176
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177 **Documentation and Repository**
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178
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179 This Galaxy wrapper of DEWSeq_ is based on the R markdown file found here (including a description of parameters):
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180
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181 https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers/tree/master/Parametrized_Rmd
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182
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183
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184 .. _DEWSeq: https://bioconductor.org/packages/release/bioc/html/DEWSeq.html
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185 .. _htseq-clip: https://github.com/EMBL-Hentze-group/htseq-clip
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186
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187 ]]></help>
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188 <citations>
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189 <citation type="bibtex">
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190 @incollection{sahadevan2022pipeline,
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191 doi={0.1007/978-1-0716-1851-6_10},
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192 url={https://doi.org/10.1007/978-1-0716-1851-6_10},
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193 title={A Pipeline for Analyzing eCLIP and iCLIP Data with Htseq-clip and DEWSeq},
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194 author={Sahadevan, Sudeep and Sekaran, Thileepan and Schwarzl, Thomas},
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195 booktitle={Post-Transcriptional Gene Regulation},
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196 pages={189--205},
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197 year={2022},
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198 publisher={Springer}
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199 }
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200 </citation>
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201 </citations>
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202 </tool>