Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.xml @ 5:7d02e2e2c8fa draft

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author galaxyp
date Thu, 28 Jan 2016 18:46:22 -0500
parents ce09f1a1bbad
children cd69250e1150
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1 <tool id="PSMtoSAM" name="PSM to SAM" version="1.3.2">
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2 <description>Generate SAM files from PSMs.</description>
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Job Failed" />
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5 </stdio>
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6 <command interpreter="Rscript --vanilla">PSM2SAM.R
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8 --passedPSM="$input"
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9 --XScolumn="$scoreColumn"
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10 --header="$samHeaders"
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11 --OutputFile="$output"
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13 #if str($genome_annotation.source) == "history":
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14 --exon_anno="$genome_annotation.exonAnno"
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15 --proteinseq="$genome_annotation.proteinSeq"
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16 --procodingseq="$genome_annotation.proCodingSeq"
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17 #else:
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18 #set index_path = $genome_annotation.builtin.fields.path
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19 --exon_anno="$index_path/exon_anno.RData"
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20 --proteinseq="$index_path/proseq.RData"
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21 --procodingseq="$index_path/procodingseq.RData"
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22 #end if
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24 2&gt;&amp;1</command>
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25 <inputs>
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26 <param name="input" type="data" format="idpdb" help="An IDPicker idpDB file to convert to SAM" label="Input PSMs">
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27 <validator type="empty_field" message="This field is required."/>
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28 </param>
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29 <param name="scoreColumn" type="text" help="The name of a PSM score to include in the SAM output (e.g. &quot;MyriMatch:mvh&quot;)" size="60" label="Score Name">
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30 <validator type="empty_field" message="This field is required."/>
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31 </param>
3
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32
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33 <conditional name="genome_annotation">
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34 <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
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35 <option value="builtin">Use a built-in genome annotation</option>
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36 <option value="history">Use annotation from your history</option>
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37 </param>
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38 <when value="builtin">
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39 <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
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40 <options from_data_table="customProDB">
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41 <filter type="sort_by" column="2"/>
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42 <validator type="no_options" message="No annotations are available for the selected input dataset"/>
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43 </options>
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44 </param>
2
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45 </when>
3
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46 <when value="history">
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47 <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
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48 <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
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49 <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
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50 </when>
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51 </conditional>
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52 <param name="samHeaders" type="data" format="txt" help="A text file of SAM headers extracted from the original SAM/BAM file or reference genome" label="SAM/BAM Headers">
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53 <validator type="empty_field" message="This field is required."/>
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54 </param>
0
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55 </inputs>
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56 <outputs>
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57 <data format="sam" name="output" label="${input.name.rsplit('.',1)[0]}.sam"/>
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58 </outputs>
3
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59 <tests>
0
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60 <test>
3
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61 <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB" />
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62 <param name="scoreColumn" value="Myrimatch:MVH" />
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63 <param name="source" value="history" />
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64 <param name="exonAnno" value="exon_anno.RData" />
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65 <param name="proteinSeq" value="proseq.RData" />
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66 <param name="proCodingSeq" value="procodingseq.RData" />
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67 <param name="samHeaders" value="header_refseq_hg19.txt" />
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68 <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
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69 </test>
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70 <test>
3
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71 <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB" />
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72 <param name="scoreColumn" value="Myrimatch:MVH" />
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73 <param name="source" value="history" />
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74 <param name="exonAnno" value="exon_anno.RData" />
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75 <param name="proteinSeq" value="proseq.RData" />
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76 <param name="proCodingSeq" value="procodingseq.RData" />
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77 <param name="samHeaders" value="header_refseq_hg19.txt" />
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78 <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
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79 </test>
3
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80 </tests>
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81 <help>
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82 **Description**
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83
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84 Generate SAM files from confident peptide-spectrum-matches (PSMs).
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85 </help>
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86 </tool>