Mercurial > repos > bgruening > salmon
annotate salmonquant.xml @ 20:f4d5237a84f6 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
author | bgruening |
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date | Mon, 18 Mar 2024 09:35:41 +0000 |
parents | c8903f357804 |
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rev | line source |
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17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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1 <tool id="salmon" name="Salmon quant" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> |
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4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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2 <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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3 <macros> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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4 <import>macros.xml</import> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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5 </macros> |
20
f4d5237a84f6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents:
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6 <expand macro="xrefs"/> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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7 <expand macro="requirements"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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8 <command detect_errors="aggressive"><![CDATA[ |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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9 #if $quant_type.qtype == "reads": |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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10 @indexing@ |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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11 @salreads@ |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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12 #else: |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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13 @salalign@ |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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14 #end if |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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15 @salquant@ |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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16 #if $quant_type.qtype == "reads" and $quant_type.bam_options.writeMappings: |
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e3d32471da11
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
bgruening
parents:
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17 && @bam_sort@ ./output/samout.sam |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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18 #end if |
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e3d32471da11
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
bgruening
parents:
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19 #if $quant_type.qtype == "alignment" and $quant_type.sampleOut: |
e3d32471da11
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664"
bgruening
parents:
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20 && @bam_sort@ ./output/postSample.bam |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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21 #end if |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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22 ]]> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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23 </command> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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24 <inputs> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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25 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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26 <param name="qtype" type="select" label="Select salmon quantification mode:"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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27 <option value="reads" selected="True">Reads</option> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
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28 <option value="alignment">Alignment</option> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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29 </param> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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30 <when value="reads"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
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31 <expand macro="index"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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32 <expand macro="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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33 </when> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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34 <when value="alignment"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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35 <expand macro="align"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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36 </when> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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37 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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38 <expand macro="quantboth"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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39 </inputs> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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40 <outputs> |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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41 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string}: transcript quantification" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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42 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string}: gene quantification"> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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43 <filter>geneMap</filter> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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44 </data> |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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45 <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string}: BAM"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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46 <filter>quant_type['qtype'] == "reads" and quant_type['bam_options']['writeMappings']</filter> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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47 </data> |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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48 <data name="postSample" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string}: sampled input alignments"> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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49 <filter>quant_type['qtype'] == "alignment" and quant_type['sampleOut']</filter> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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50 </data> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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51 </outputs> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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52 <tests> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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53 <test expect_num_outputs="2"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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54 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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55 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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56 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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57 <param name="TranscriptSource" value="history"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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58 <section name="s_index"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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59 <param name="fasta" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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60 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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61 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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62 <section name="input"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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63 <conditional name="single_or_paired"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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64 <param name="single_or_paired_opts" value="paired" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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65 <param name="input_mate1" value="fastqs/reads_1.fastq" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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66 <param name="input_mate2" value="fastqs/reads_2.fastq" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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67 <conditional name="libtype"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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68 <param name="strandedness" value="U"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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69 </conditional> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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70 </conditional> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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71 </section> |
17
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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72 <conditional name="bam_options"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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73 <param name="writeMappings" value="--writeMappings=./output/samout.sam"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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74 </conditional> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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75 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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76 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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77 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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78 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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79 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
80 <has_text text="NM_001168316" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
81 <has_text text="NM_174914" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
82 <has_text text="NM_018953" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
83 <has_text text="NR_003084" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
84 <has_text text="NM_017410" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
85 <has_text text="NM_153693" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
86 <has_text text="NR_031764" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
87 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
88 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
89 </output> |
16
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
90 <assert_command> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
91 <has_text text="--libType IU"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
92 </assert_command> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
93 </test> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
94 <test expect_num_outputs="2"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
95 <conditional name="quant_type"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
96 <param name="qtype" value="reads"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
97 <conditional name="refTranscriptSource"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
98 <param name="TranscriptSource" value="history"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
99 <section name="s_index"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
100 <param name="fasta" value="transcripts.fasta"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
101 </section> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
102 </conditional> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
103 <section name="input"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
104 <param name="single_or_paired.single_or_paired_opts" value="paired" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
105 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
106 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
107 </section> |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
16
diff
changeset
|
108 <conditional name="bam_options"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
16
diff
changeset
|
109 <param name="writeMappings" value="--writeMappings=./output/samout.sam"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
16
diff
changeset
|
110 </conditional> |
16
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
111 </conditional> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
112 <output name="output_quant" ftype="tabular"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
113 <assert_contents> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
114 <has_text text="EffectiveLength" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
115 <has_text text="TPM" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
116 <has_text text="NM_001168316" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
117 <has_text text="NM_174914" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
118 <has_text text="NM_018953" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
119 <has_text text="NR_003084" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
120 <has_text text="NM_017410" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
121 <has_text text="NM_153693" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
122 <has_text text="NR_031764" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
123 <has_n_columns n="5" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
124 </assert_contents> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
125 </output> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
126 <assert_command> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
127 <has_text text="--libType A"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
13
diff
changeset
|
128 </assert_command> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
129 </test> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
130 <test expect_num_outputs="1"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
131 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
132 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
133 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
134 <param name="TranscriptSource" value="history"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
135 <section name="s_index"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
136 <param name="fasta" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
137 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
138 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
139 <section name="input"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
140 <param name="single_or_paired.single_or_paired_opts" value="paired" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
141 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq.gz" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
142 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq.gz" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
143 <param name="single_or_paired.strandedness" value="U"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
144 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
145 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
146 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
147 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
148 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
149 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
150 <has_text text="NM_001168316" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
151 <has_text text="NM_174914" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
152 <has_text text="NM_018953" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
153 <has_text text="NR_003084" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
154 <has_text text="NM_017410" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
155 <has_text text="NM_153693" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
156 <has_text text="NR_031764" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
157 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
158 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
159 </output> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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160 </test> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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161 <test expect_num_outputs="1"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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162 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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163 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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164 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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165 <param name="TranscriptSource" value="history"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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166 <section name="s_index"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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167 <param name="fasta" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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168 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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169 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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170 <section name="input"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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171 <param name="single_or_paired.single_or_paired_opts" value="single" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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172 <param name="single_or_paired.input_mate1" value="fastqs/reads_both.fastq.bz2" /> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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173 <param name="single_or_paired.strandedness" value="U"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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174 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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175 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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176 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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177 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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178 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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179 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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180 <has_text text="NM_001168316" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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181 <has_text text="NM_174914" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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182 <has_text text="NM_018953" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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183 <has_text text="NR_003084" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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184 <has_text text="NM_017410" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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185 <has_text text="NM_153693" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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186 <has_text text="NR_031764" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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187 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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188 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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189 </output> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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190 </test> |
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c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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191 <!-- Test 05 --> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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192 <test expect_num_outputs="2"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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193 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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194 <param name="qtype" value="alignment"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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195 <param name="afile" value="salmonbam.bam"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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196 <param name="transcript" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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197 <param name="sampleOut" value="--sampleOut"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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198 <param name="sampleUnaligned" value="--sampleUnaligned"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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199 <param name="noErrorModel" value="--noErrorModel"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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200 <param name="numErrorBins" value="5"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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201 </conditional> |
16
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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202 <!-- bam output uses non-deterministic sampling, so can only use compare="sim_size" --> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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203 <output name="postSample" ftype="bam" value="postSample.bam" compare="sim_size" delta="20000"/> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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204 <assert_stderr> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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205 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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206 </assert_stderr> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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207 </test> |
16
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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208 <test expect_num_outputs="2"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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209 <conditional name="quant_type"> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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210 <param name="qtype" value="alignment"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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211 <param name="afile" value="salmonbam.bam"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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212 <param name="ont" value="true" /> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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213 <param name="transcript" value="transcripts.fasta"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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214 <param name="sampleOut" value="--sampleOut"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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215 <param name="sampleUnaligned" value="--sampleUnaligned"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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216 <param name="noErrorModel" value="--noErrorModel"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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217 <param name="numErrorBins" value="5"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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218 </conditional> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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219 <assert_stderr> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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220 <has_text text="Sampling alignments; outputting results to ./output/postSample.bam"/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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221 </assert_stderr> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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222 <assert_command> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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223 <has_text text=" --ont "/> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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224 </assert_command> |
49121db48873
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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225 </test> |
10
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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226 <test expect_num_outputs="1"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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227 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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228 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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229 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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230 <param name="TranscriptSource" value="history"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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231 <section name="s_index"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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232 <param name="fasta" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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233 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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234 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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235 <section name="input"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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236 <param name="single_or_paired.single_or_paired_opts" value="paired" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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237 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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238 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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|
239 <param name="single_or_paired.strandeness" value="U"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
240 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
241 <param name="discardOrphansQuasi" value="-discardOrphansQuasi"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
242 <conditional name="validmap"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
243 <param name="validateMappings" value="--validateMappings"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
244 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
245 <param name="dovetail" value="--allowDovetail"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
246 <param name="recoverOrphans" value="--recoverOrphans"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
247 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
248 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
249 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
250 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
251 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
252 <has_text text="NM_001168316" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
253 <has_text text="NM_174914" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
254 <has_text text="NM_018953" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
255 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
256 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
257 </output> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
258 </test> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
259 <test expect_num_outputs="1"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
260 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
261 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
262 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
263 <param name="TranscriptSource" value="history"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
264 <section name="s_index"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
265 <param name="fasta" value="transcripts.fasta"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
266 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
267 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
268 <section name="input"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
269 <param name="single_or_paired.single_or_paired_opts" value="paired" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
270 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
271 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
272 <param name="single_or_paired.strandedness" value="U"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
273 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
274 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
275 <param name="seqBias" value="--seqBias"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
276 <param name="gcBias" value="--gcBias"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
277 <section name="adv"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
278 <param name="dumpEq" value="--dumpEq"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
279 <param name="minAssignedFrags" value="10"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
280 <param name="noLengthCorrection"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
281 <param name="initUniform" value="--initUniform"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
282 <param name="useEM" value="--useEM"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
283 <param name="noGammaDraw" value="--noGammaDraw"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
284 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
285 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
286 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
287 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
288 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
289 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
290 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
291 </output> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
292 </test> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
293 <test expect_num_outputs="1"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
294 <conditional name="quant_type"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
295 <param name="qtype" value="reads"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
296 <conditional name="refTranscriptSource"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
297 <param name="TranscriptSource" value="indexed"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
298 <param name="index" value="hg19_transcript_subset" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
299 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
300 <section name="input"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
301 <conditional name="single_or_paired"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
302 <param name="single_or_paired_opts" value="paired" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
303 <param name="input_mate1" value="fastqs/reads_1.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
304 <param name="input_mate2" value="fastqs/reads_2.fastq" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
305 <param name="strandedness" value="U"/> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
306 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
307 </section> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
308 </conditional> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
309 <output name="output_quant" ftype="tabular"> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
310 <assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
311 <has_text text="EffectiveLength" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
312 <has_text text="TPM" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
313 <has_text text="NM_001168316" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
314 <has_text text="NM_174914" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
315 <has_text text="NM_018953" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
316 <has_text text="NR_003084" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
317 <has_text text="NM_017410" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
318 <has_text text="NM_153693" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
319 <has_text text="NR_031764" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
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changeset
|
320 <has_n_columns n="5" /> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
321 </assert_contents> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
322 </output> |
4de6e2e40c7a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
323 </test> |
17
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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324 <!-- Test 10 --> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
325 <!-- Test writeQualities option--> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
326 <test expect_num_outputs="2"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
327 <conditional name="quant_type"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
328 <param name="qtype" value="reads"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
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329 <conditional name="refTranscriptSource"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
330 <param name="TranscriptSource" value="history"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
331 <section name="s_index"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
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332 <param name="fasta" value="transcripts.fasta"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
333 </section> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
334 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
335 <section name="input"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
336 <param name="single_or_paired.single_or_paired_opts" value="paired" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
337 <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
338 <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
339 </section> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
340 <conditional name="bam_options"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
341 <param name="writeMappings" value="--writeMappings=./output/samout.sam"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
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342 <param name="writeQualities" value="true"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
343 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
344 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
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345 <output name="output_quant" ftype="tabular"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
346 <assert_contents> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
347 <has_text text="EffectiveLength" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
348 <has_text text="TPM" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
349 <has_text text="NM_001168316" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
350 <has_text text="NM_174914" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
351 <has_text text="NM_018953" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
352 <has_text text="NR_003084" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
353 <has_text text="NM_017410" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
354 <has_text text="NM_153693" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
355 <has_text text="NR_031764" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
356 <has_n_columns n="5" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
357 </assert_contents> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
358 </output> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
359 <assert_command> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
360 <has_text text="--libType A"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
361 </assert_command> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
362 </test> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
363 <!-- Test genome input for decoy index --> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
364 <test expect_num_outputs="2"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
365 <conditional name="quant_type"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
366 <param name="qtype" value="reads"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
367 <conditional name="refTranscriptSource"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
368 <param name="TranscriptSource" value="history"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
369 <section name="s_index"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
370 <param name="fasta" value="transcripts.fasta"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
371 <param name="genome" value="genome.fasta"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
372 </section> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
373 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
374 <section name="input"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
375 <conditional name="single_or_paired"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
376 <param name="single_or_paired_opts" value="paired" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
377 <param name="input_mate1" value="fastqs/reads_1.fastq" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
378 <param name="input_mate2" value="fastqs/reads_2.fastq" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
379 <conditional name="libtype"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
380 <param name="strandedness" value="U"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
381 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
382 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
383 </section> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
384 <conditional name="bam_options"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
385 <param name="writeMappings" value="--writeMappings=./output/samout.sam"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
386 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
387 </conditional> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
388 <output name="output_quant" ftype="tabular"> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
389 <assert_contents> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
390 <has_text text="EffectiveLength" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
391 <has_text text="TPM" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
392 <has_text text="NM_001168316" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
393 <has_text text="NM_174914" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
394 <has_text text="NM_018953" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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changeset
|
395 <has_text text="NR_003084" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
396 <has_text text="NM_017410" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
397 <has_text text="NM_153693" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
398 <has_text text="NR_031764" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
399 <has_n_columns n="5" /> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
400 </assert_contents> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
401 </output> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
402 <assert_command> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
403 <has_text text="--libType IU"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
404 <has_text text="--decoy"/> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
405 </assert_command> |
c8903f357804
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
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diff
changeset
|
406 </test> |
20
f4d5237a84f6
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
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407 <!-- test 12: interleaved input --> |
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408 <test expect_num_outputs="2"> |
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409 <conditional name="quant_type"> |
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410 <param name="qtype" value="reads"/> |
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411 <conditional name="refTranscriptSource"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
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412 <param name="TranscriptSource" value="history"/> |
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413 <section name="s_index"> |
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414 <param name="fasta" value="transcripts.fasta"/> |
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415 </section> |
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416 </conditional> |
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417 <section name="input"> |
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418 <conditional name="single_or_paired"> |
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419 <param name="single_or_paired_opts" value="paired_interleaved" /> |
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420 <param name="input_1" value="fastqs/reads_both.fastq.bz2" /> |
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421 <conditional name="libtype"> |
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422 <param name="strandedness" value="U"/> |
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423 </conditional> |
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424 </conditional> |
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425 </section> |
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426 <conditional name="bam_options"> |
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427 <param name="writeMappings" value="--writeMappings=./output/samout.sam"/> |
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428 </conditional> |
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429 </conditional> |
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430 <output name="output_quant" ftype="tabular"> |
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431 <assert_contents> |
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432 <has_text text="EffectiveLength" /> |
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433 <has_text text="TPM" /> |
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434 <has_text text="NM_001168316" /> |
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435 <has_text text="NM_174914" /> |
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436 <has_text text="NM_018953" /> |
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437 <has_text text="NR_003084" /> |
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438 <has_text text="NM_017410" /> |
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439 <has_text text="NM_153693" /> |
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440 <has_text text="NR_031764" /> |
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441 <has_n_columns n="5" /> |
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442 </assert_contents> |
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443 </output> |
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444 <assert_command> |
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445 <has_text text="--libType IU"/> |
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446 </assert_command> |
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447 </test> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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448 </tests> |
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449 <help><![CDATA[ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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450 @salmonhelp@ |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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451 ]]></help> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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452 <expand macro="citations"/> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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453 </tool> |