Re: [galaxy-dev] Running a different command based on selection in the tool
Hi Saba and Jens, : are not needed, they are optional, see http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTION00068 Maybe it's a problem with the left quotes around Use_Snapshot in the #if line? Nicola Il 2014-03-20 06:26 Keilwagen, Jens ha scritto: Hi Saba, there is a syntax error in the line of the #if. Please add : at the end and report whether the error still occurs. All the best, Jens VON: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for m input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=w type=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=z type=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Running a different command based on selection in the tool
Hi all, It may be the comparison, I've sometimes found an explicit cast to str is required in this kind of situation. So, I would try: command #if str($source.source_select)==Use_Snapshot: cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command Regards, Peter On Thu, Mar 20, 2014 at 10:17 AM, Nicola Soranzo sora...@crs4.it wrote: Hi Saba and Jens, : are not needed, they are optional, see http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTION00068 Maybe it's a problem with the left quotes around Use_Snapshot in the #if line? Nicola Il 2014-03-20 06:26 Keilwagen, Jens ha scritto: Hi Saba, there is a syntax error in the line of the #if. Please add : at the end and report whether the error still occurs. All the best, Jens VON: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for m input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=w type=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=z type=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Running a different command based on selection in the tool
Hi all, For all the input parameters, we have to explicitly use $source.input, $source.m, etc instead of just using input, m, etc. Please see the code below that works. command #if $source.source_select==Use_Snapshot ./cM-snapshot.sh $source.input $output #else ./cM.sh $source.m $source.b $source.ns $source.w $source.s $source.z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=wtype=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=ztype=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional Thanks, Saba On Mar 20, 2014, at 5:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, It may be the comparison, I've sometimes found an explicit cast to str is required in this kind of situation. So, I would try: command #if str($source.source_select)==Use_Snapshot: cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command Regards, Peter On Thu, Mar 20, 2014 at 10:17 AM, Nicola Soranzo sora...@crs4.it wrote: Hi Saba and Jens, : are not needed, they are optional, see http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTION00068 Maybe it's a problem with the left quotes around Use_Snapshot in the #if line? Nicola Il 2014-03-20 06:26 Keilwagen, Jens ha scritto: Hi Saba, there is a syntax error in the line of the #if. Please add : at the end and report whether the error still occurs. All the best, Jens VON: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for m input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=w type=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=z type=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Running a different command based on selection in the tool
Hi Saba, there is a syntax error in the line of the #if. Please add : at the end and report whether the error still occurs. All the best, Jens Von: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Im Auftrag von Saba Sehrish Gesendet: Mittwoch, 19. März 2014 23:07 An: galaxy-dev@lists.bx.psu.edu Betreff: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for m input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba command #if $source.source_select==Use_Snapshot cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if /command inputs conditional name=source param name=source_select type=select label=Specify the input option value=Use_SnapshotUse Snapshot/option option value=Set_ValuesSet Values/option /param when value=Use_Snapshot param name=input type=data format=dbm size=100 label=Input Snapshot/ sanitizer sanitize=False/ /when when value=Set_Values param name=m label=Omega_m h^2 type=float value=0.1279 min=0.120 max=0.155/ param name=b label=Omega_b h^2 type=float value=0.0232 min=0.0215 max=0.0235/ param name=ns label=n_s type=float value=0.8629 min=0.85 max=1.05/ param name=w label=wtype=float value=-1.184 min=-1.30 max=-0.70/ param name=s label=sigma_8 type=float value=0.6159 min=0.61 max=0.9/ param name=z label=ztype=float value=1.0 min=0.0 max=1.0/ sanitizer sanitize=False/ /when /conditional /inputs ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
