Mercurial > repos > nml > sistr_cmd
diff sistr_cmd.xml @ 4:17fcac7ddf54 draft
"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
| author | nml |
|---|---|
| date | Thu, 06 Aug 2020 11:48:49 -0400 |
| parents | 5c8ff92e38a9 |
| children | 24a7a95867b0 |
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--- a/sistr_cmd.xml Wed Jun 14 14:36:59 2017 -0400 +++ b/sistr_cmd.xml Thu Aug 06 11:48:49 2020 -0400 @@ -1,9 +1,12 @@ -<tool id="sistr_cmd" name="sistr_cmd" version="1.0.2"> +<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@"> <description> - Salmonella In Silico Typing Resource commandline tool for serovar prediction + Salmonella In Silico Typing Resource commandline tool for serovar prediction </description> + <macros> + <token name="@VERSION@">1.1.1</token> + </macros> <requirements> - <requirement type="package" version="1.0.2">sistr_cmd</requirement> + <requirement type="package" version="@VERSION@">sistr_cmd</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -161,38 +164,42 @@ </outputs> <tests> <test> - <param name="input_fastas" value="AE014613-699860.fasta"/> + <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/> <param name="output_format" value="tab"/> <output name="cgmlst_profiles" value="cgmlst-profiles.csv" ftype="csv" - lines_diff="2"> - <assert_contents> - <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/> - </assert_contents> + compare="diff"> </output> - <output - name="output_prediction_tab" - value="sistr-results.tab" + <output name="output_prediction_tab" ftype="tabular" - lines_diff="2"> + value="sistr-results.tabular" + compare="sim_size"> <assert_contents> <has_text text="AE014613-699860" /> <has_text text="Typhi" /> <has_text text="enterica" /> - <has_text text="-:-:-" /> - <has_n_columns n="21" /> + <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/> + <has_text text="2014-LET-0419"/> + <has_n_columns n="22" /> </assert_contents> </output> <output name="alleles_output" value="alleles-output.json" ftype="json" - compare="sim_size"/> + compare="sim_size"> + <assert_contents> + <has_text text="NZ_AOXE01000059.1"/> + <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/> + <has_text text="NZ_AOXE01000033.1"/> + <has_text text="NZ_AOXE01000052.1"/> + </assert_contents> + </output> </test> <test> - <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> + <param name="input_fastas" value="13-1101-Paratyphi_B.fasta" ftype="fasta"/> <param name="output_format" value="tab"/> <output name="novel_alleles" @@ -203,79 +210,32 @@ name="cgmlst_profiles" value="cgmlst-profiles-13-1101.csv" ftype="csv" - lines_diff="2"> + compare="diff"> </output> <output name="output_prediction_tab" - value="sistr-results-13-1101.tab" + value="sistr-results-13-1101.tabular" ftype="tabular" - lines_diff="2"> + compare="sim_size"> <assert_contents> - <has_text text="13-1101-Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> - <has_n_columns n="21" /> + <has_text text="13-1101-Paratyphi_B"/> + <has_text text="Paratyphi B var. Java"/> + <has_text text="enterica"/> + <has_text text="1,4,[5],12"/> + <has_text text="PASS"/> + <has_n_columns n="22"/> </assert_contents> </output> <output name="alleles_output" value="alleles-output-13-1101.json" ftype="json" - compare="sim_size"/> - </test> - <test> - <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/> - <param name="output_format" value="tab"/> - <output - name="novel_alleles" - value="novel-alleles-13-1101.fasta" - ftype="fasta" - compare="sim_size"/> - <output - name="cgmlst_profiles" - value="cgmlst-profiles-13-1101.csv" - ftype="csv" - lines_diff="2"> - </output> - <output - name="output_prediction_tab" - value="sistr-results-13-1101.tab" - ftype="tabular" - lines_diff="2"> - <assert_contents> - <has_text text="13-1101 Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> - <has_n_columns n="21" /> - </assert_contents> - </output> - <output - name="alleles_output" - value="alleles-output-13-1101.json" - ftype="json" - compare="sim_size"/> - </test> - <test> - <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> - <param name="output_format" value="json"/> - <param name="more_output" value="-MM"/> - <output - name="output_prediction_json" - value="sistr-results-13-1101.json" - ftype="json" compare="sim_size"> <assert_contents> - <has_text text="13-1101-Paratyphi_B" /> - <has_text text="Paratyphi B var. Java" /> - <has_text text="enterica" /> - <has_text text="1,4,[5],12" /> - <has_text text="PASS" /> + <has_text text="13-1101-Paratyphi_B"/> + <has_text text="NZ_AOXE01000059.1"/> </assert_contents> - </output> + </output> </test> </tests> <help>