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annotate salmonquant.xml @ 12:2e3425b9f01d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
author bgruening
date Mon, 09 Sep 2019 10:37:28 -0400
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children 818b16dd05a1
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12
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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1 <tool id="salmon" name="Salmon quant" version="@VERSION@">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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2 <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive"><![CDATA[
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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8 #if $quant_type.qtype == "reads":
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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9 @indexing@
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10 @salreads@
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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11 #else:
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12 @salalign@
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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13 #end if
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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14 @salquant@
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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15 #if $quant_type.qtype == "reads":
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16 #if $quant_type.writeMappings:
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17 && samtools view -S -b ./output/samout.sam > ./output/bamout.bam
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18 #end if
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19 #end if
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20 #if $quant_type.qtype == "alignment":
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21 #if $quant_type.sampleOut:
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22 && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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23 #end if
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24 #end if
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25 ]]>
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26 </command>
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27 <inputs>
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28 <conditional name="quant_type">
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29 <param name="qtype" type="select" label="Select salmon quantification mode:">
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30 <option value="reads" selected="True">Reads</option>
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31 <option value="alignment">Alignment</option>
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32 </param>
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33 <when value="reads">
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34 <expand macro="index"/>
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35 <expand macro="reads"/>
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36 </when>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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37 <when value="alignment">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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38 <expand macro="align"/>
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39 </when>
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40 </conditional>
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41 <expand macro="quantboth"/>
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42 </inputs>
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43 <outputs>
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44 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
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45 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
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46 <filter>geneMap</filter>
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47 </data>
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48 <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">
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49 <filter>quant_type['qtype'] == "reads" and quant_type['writeMappings']</filter>
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50 </data>
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51 <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)">
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52 <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="2">
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57 <conditional name="quant_type">
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58 <param name="qtype" value="reads"/>
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59 <conditional name="refTranscriptSource">
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60 <param name="TranscriptSource" value="history"/>
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61 <section name="s_index">
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62 <param name="fasta" value="transcripts.fasta"/>
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63 </section>
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64 </conditional>
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65 <section name="input">
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66 <param name="single_or_paired.single_or_paired_opts" value="paired" />
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67 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
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68 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
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69 <param name="single_or_paired.strandedness" value="U"/>
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70 </section>
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71 <param name="writeMappings" value="true"/>
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72 </conditional>
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73 <output name="output_quant" ftype="tabular">
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74 <assert_contents>
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75 <has_text text="EffectiveLength" />
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76 <has_text text="TPM" />
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77 <has_text text="NM_001168316" />
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78 <has_text text="NM_174914" />
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79 <has_text text="NM_018953" />
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80 <has_text text="NR_003084" />
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81 <has_text text="NM_017410" />
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82 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
83 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
84 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
85 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
86 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
87 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
88 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
89 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
90 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
91 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
92 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
93 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
94 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
95 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
96 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
97 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
98 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
99 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq.gz" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
100 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq.gz" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
101 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
102 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
103 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
104 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
105 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
106 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
107 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
108 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
109 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
110 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
111 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
112 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
113 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
114 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
115 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
116 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
117 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
118 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
119 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
120 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
121 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
122 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
123 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
124 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
125 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
126 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
127 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
128 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
129 <param name="single_or_paired.single_or_paired_opts" value="single" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
130 <param name="single_or_paired.input_mate1" value="fastqs/reads_both.fastq.bz2" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
131 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
132 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
133 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
134 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
135 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
136 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
137 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
138 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
139 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
140 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
141 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
142 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
143 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
144 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
145 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
146 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
147 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
148 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
149 <test expect_num_outputs="2">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
150 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
151 <param name="qtype" value="alignment"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
152 <param name="afile" value="salmonbam.bam"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
153 <param name="transcript" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
154 <param name="sampleOut" value="--sampleOut"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
155 <param name="sampleUnaligned" value="--sampleUnaligned"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
156 <param name="noErrorModel" value="--noErrorModel"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
157 <param name="numErrorBins" value="5"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
158 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
159 <output name="postSample" ftype="bam" value="postSample.bam"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
160 <assert_stderr>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
161 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
162 </assert_stderr>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
163 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
164 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
165 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
166 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
167 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
168 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
169 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
170 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
171 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
172 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
173 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
174 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
175 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
176 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
177 <param name="single_or_paired.strandeness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
178 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
179 <param name="discardOrphansQuasi" value="-discardOrphansQuasi"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
180 <conditional name="validmap">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
181 <param name="validateMappings" value="--validateMappings"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
182 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
183 <param name="dovetail" value="--allowDovetail"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
184 <param name="recoverOrphans" value="--recoverOrphans"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
185 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
186 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
187 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
188 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
189 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
190 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
191 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
192 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
193 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
194 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
195 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
196 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
197 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
198 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
199 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
200 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
201 <param name="TranscriptSource" value="history"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
202 <section name="s_index">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
203 <param name="fasta" value="transcripts.fasta"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
204 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
205 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
206 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
207 <param name="single_or_paired.single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
208 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
209 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
210 <param name="single_or_paired.strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
211 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
212 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
213 <param name="seqBias" value="--seqBias"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
214 <param name="gcBias" value="--gcBias"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
215 <section name="adv">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
216 <param name="dumpEq" value="--dumpEq"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
217 <param name="minAssignedFrags" value="10"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
218 <param name="noLengthCorrection"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
219 <param name="initUniform" value="--initUniform"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
220 <param name="useEM" value="--useEM"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
221 <param name="noGammaDraw" value="--noGammaDraw"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
222 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
223 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
224 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
225 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
226 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
227 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
228 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
229 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
230 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
231 <test expect_num_outputs="1">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
232 <conditional name="quant_type">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
233 <param name="qtype" value="reads"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
234 <conditional name="refTranscriptSource">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
235 <param name="TranscriptSource" value="indexed"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
236 <param name="index" value="hg19_transcript_subset" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
237 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
238 <section name="input">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
239 <conditional name="single_or_paired">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
240 <param name="single_or_paired_opts" value="paired" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
241 <param name="input_mate1" value="fastqs/reads_1.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
242 <param name="input_mate2" value="fastqs/reads_2.fastq" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
243 <param name="strandedness" value="U"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
244 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
245 </section>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
246 </conditional>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
247 <output name="output_quant" ftype="tabular">
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
248 <assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
249 <has_text text="EffectiveLength" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
bgruening
parents:
diff changeset
250 <has_text text="TPM" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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251 <has_text text="NM_001168316" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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252 <has_text text="NM_174914" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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253 <has_text text="NM_018953" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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254 <has_text text="NR_003084" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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255 <has_text text="NM_017410" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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256 <has_text text="NM_153693" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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257 <has_text text="NR_031764" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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258 <has_n_columns n="5" />
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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259 </assert_contents>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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260 </output>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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261 </test>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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262 </tests>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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263 <help><![CDATA[
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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264 @salmonhelp@
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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265 ]]></help>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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266 <expand macro="citations"/>
2e3425b9f01d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 06db9bd0914a60c3ddc0a1f77de0d6f731b56e02"
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267 </tool>