diff peptide_shaker.xml @ 32:ff592231f118 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d

--- a/peptide_shaker.xml	Wed Jan 18 16:43:44 2017 -0500
+++ b/peptide_shaker.xml	Wed Jan 25 15:37:43 2017 -0500
@@ -337,8 +337,12 @@
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
             <param name="outputs" value="zip,3"/>
-            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />
-            <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
+            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
+            <output name="output_psm">
+                <assert_contents>
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
@@ -346,14 +350,53 @@
             <param name="filtering_options_selector" value="yes"/>
             <param name="min_peptide_length" value="1"/>
             <param name="outputs" value="0,1,2,3,4,5,6,7"/>
-            <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
-            <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
-            <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
-            <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
-            <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
-            <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
-            <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
-            <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
+            <output name="output_certificate">
+                <assert_contents>
+                    <has_text text="Tolerance: 100" />
+                    <has_text text="Carbamidomethylation of C" />
+                </assert_contents>
+            </output>
+            <output name="output_hierarchical">
+                <assert_contents>
+                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
+                </assert_contents>
+            </output>
+            <output name="output_psm">
+                <assert_contents>
+                    <not_has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_psm_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_peptides">
+                <assert_contents>
+                    <has_text text="Modification" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_peptides_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_proteins">
+                <assert_contents>
+                    <has_text text="Modification" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+            <output name="output_proteins_phosphorylation">
+                <assert_contents>
+                    <has_text text="Phosphosite" />
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help>